Essential amino acids (EAA) play an important role in promoting milk protein synthesis in primary bovine mammary epithelial cells (BMEC). However, the regulatory mechanisms involved in the relationship between EAA and milk protein synthesis have not been fully explored. This study examined the effects of seryl-tRNA synthetase (SARS) on EAA-stimulated β-casein synthesis, cell proliferation, and the mammalian target of rapamycin (mTOR) system in BMEC. First, BMEC were cultured in medium either lacking all EAA (-EAA) or that included all EAA (+EAA) for 12 h. The BMEC were then supplemented with the opposing treatments (-EAA supplemented with +EAA and vice versa) for 0 h, 10 min, 0.5 h, 1 h, 6 h, or 12 h, respectively. After the treatment-specific time allotment, proteins were collected for Western blotting. Subsequently, a 2 × 2 factorial design was used to evaluate the interactive of SARS inhibition (control or SARS inhibited) and EAA supply (+EAA or -EAA) on gene and protein abundance, cell viability, and cell cycle in BMEC. Based on the data obtained in the first experiment, the changes in protein abundance of β-casein and SARS depended on EAA treatment time in similar patterns. The protein abundance of β-casein, SARS, and mammalian target of rapamycin (mTOR)-related proteins, cell viability, cell cycle progression, and the mRNA abundance of cyclin D1 (CCND1, cell cycle progression marker) and marker of proliferation Ki-67 (MKI67, cell proliferation marker) were stimulated by the presence of EAA. Correspondingly, when cells were deprived of EAA, cell proliferation and abundance of these proteins and genes were reduced overall. Moreover, the decreases in these aspects were further exacerbated by inhibiting SARS, suggesting that an interaction between EAA and SARS is important for regulating protein synthesis. The results indicated that SARS stimulated the mTOR signaling pathway when EAA were present, enhanced EAA-stimulated cell proliferation, and contributed to increased β-casein production in BMEC.

The mechanisms driving innovations that distinguish large taxons are poorly known and essentially accessible via a candidate gene approach. A spectacular acquisition by tunicate larvaceans is the house, a complex extracellular filtration device. Its components are secreted by the oikoplastic epithelium which covers the animal trunk. Here we describe the development of this epithelium in larvae through the formation of specific cellular territories known to produce distinct sets of house proteins (Oikosins). It involves cell divisions and morphological differentiation but very limited cell migration. A diverse set of homeobox genes, most often duplicated in the genome, are transiently and site-specifically expressed in the trunk epithelium at early larval stages. Using RNA interference, we show that two prop duplicates are involved in the differentiation of a region on and around the dorsal midline, regulating morphology and the production of a specific oikosin. Our observations favor a scenario in which multiple homeobox genes and most likely other developmental transcription factors were recruited for this innovation. Their frequent duplications probably predated, but were not required for the emergence of the house.

Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors. 2) Mutations on the extra domain of SARS 3C-like protease can transform the active catalytic machinery into the inactive collapsed state by structurally-driven allostery. 3) Amazingly, even without detectable structural changes, mutations on the extra domain are sufficient to either inactivate or enhance the catalytic machinery of SARS 3C-like protease by dynamically-driven allostery. 4) Global networks of correlated motions have been identified: for SARS 3C-like protease, N214A inactivates the catalytic machinery by decoupling the network, while STI/A and STIF/A enhance by altering the patterns of the network. The global networks of Dengue and Zika proteases are coordinated by their NS2B-cofactors. 5) Natural products were identified to allosterically inhibit Zika and Dengue proteases through binding a pocket on the back of the active site. Therefore, by introducing extra domains/cofactors, nature develops diverse strategies to regulate the catalytic machinery embedded on the chymotrypsin fold through folding, structurally- and dynamically-driven allostery, all of which might be exploited to develop antiviral drugs.

Pandemics are large-scale outbreaks of infectious disease that can greatly increase morbidity and mortality over a wide geographic area and cause significant economic, social, and political disruption. Evidence suggests that the likelihood of pandemics has increased over the past century because of increased global travel and integration, urbanization, changes in land use, and greater exploitation of the natural environment (Jones and others 2008; Morse 1995). These trends likely will continue and will intensify. Significant policy attention has focused on the need to identify and limit emerging outbreaks that might lead to pandemics and to expand and sustain investment to build preparedness and health capacity (Smolinsky, Hamburg, and Lederberg 2003). The international community has made progress toward preparing for and mitigating the impacts of pandemics. The 2003 severe acute respiratory syndrome (SARS) pandemic and growing concerns about the threat posed by avian influenza led many countries to devise pandemic plans (U.S. Department of Health and Human Services 2005). Delayed reporting of early SARS cases also led the World Health Assembly to update the International Health Regulations (IHR) to compel all World Health Organization member states to meet specific standards for detecting, reporting on, and responding to outbreaks (WHO 2005). The framework put into place by the updated IHR contributed to a more coordinated global response during the 2009 influenza pandemic (Katz 2009). International donors also have begun to invest in improving preparedness through refined standards and funding for building health capacity (Wolicki and others 2016). Despite these improvements, significant gaps and challenges exist in global pandemic preparedness. Progress toward meeting the IHR has been uneven, and many countries have been unable to meet basic requirements for compliance (Fischer and Katz 2013; WHO 2014). Multiple outbreaks, notably the 2014 West Africa Ebola epidemic, have exposed gaps related to the timely detection of disease, availability of basic care, tracing of contacts, quarantine and isolation procedures, and preparedness outside the health sector, including global coordination and response mobilization (Moon and others 2015; Pathmanathan and others 2014). These gaps are especially evident in resource-limited settings and have posed challenges during relatively localized epidemics, with dire implications for what may happen during a full-fledged global pandemic. For the purposes of this chapter, an epidemic is defined as “the occurrence in a community or region of cases of an illness . . . clearly in excess of normal expectancy” (Porta 2014). A pandemic is defined as “an epidemic occurring over a very wide area, crossing international boundaries, and usually affecting a large number of people” (Porta 2014). Pandemics are, therefore, identified by their geographic scale rather than the severity of illness. For example, in contrast to annual seasonal influenza epidemics, pandemic influenza is defined as “when a new influenza virus emerges and spreads around the world, and most people do not have immunity” (WHO 2010). This chapter does not consider endemic diseases—those that are constantly present in particular localities or regions. Endemic diseases are far more common than pandemics and can have significant negative health and economic impacts, especially in low- and middle-income countries (LMICs) with weak health systems. Additionally, given the lack of historical data and extreme uncertainty regarding bioterrorism, this chapter does not specifically consider bioterrorism-related events, although bioterrorism could hypothetically lead to a pandemic. This chapter covers the following findings concerning the risks, impacts, and mitigation of pandemics as well as knowledge gaps:

Infectious diseases were responsible for the largest global burden of premature death and disability until the end of the twentieth century, when that distinction passed to noncommunicable diseases. Over the previous centuries, global pandemics of infectious diseases, such as smallpox, cholera, and influenza, periodically threatened the survival of entire populations. At least as early as the late 1800s, improved living conditions (such as better sanitation and piped water supplies), particularly in high-income countries (HICs), began to drive down the infectious disease burden. By the mid-twentieth century, safe, effective, and affordable vaccines and the increasing availability of antibiotics had further reduced the toll of infectious diseases in HICs. Not until the second half of the twentieth century did large-scale efforts begin to better control infectious diseases in low- and middle-income countries (LMICs), where the infectious disease burden was greatest and highly varied. These efforts included a global commitment to immunize the world’s children against the major infections for which vaccines are available and global campaigns to control malaria and diarrheal disease. The International Health Regulations of the World Health Organization (WHO) represent a key agreement among 196 countries to implement metrics and measures to detect and control outbreaks of infectious diseases and to prevent pandemics (World Health Assembly 2005). Global under-five mortality fell by almost two-thirds (from 14 percent to 5 percent) between 1970 and 2010 (Norheim and others 2015). In 1980, smallpox, responsible for 300 million–500 million deaths in the twentieth century, was declared to be the first disease eradicated from the planet following a global immunization campaign led by the WHO. Wild Poliovirus has been eliminated from all but three countries (Afghanistan, Nigeria, and Pakistan) and currently is the focus of a major eradication program. The decline of the vaccine-preventable diseases has contributed to a recognition of the potential for using vaccines to prevent other infectious diseases, including human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS), tuberculosis (TB), malaria, hepatitis C, and a variety of neglected tropical diseases (NTDs). Hepatitis B and C substantially increase the risk of death from cirrhosis and liver cancer. The effect of viral hepatitis is significant. Indeed, an important recent study (Stanaway and others 2015) found that viral hepatitis led to an estimated 0.9 million deaths in 1990 (including hepatitis-caused deaths from cirrhosis and liver cancer). Furthermore, this number has been increasing rapidly—to an estimated 1.5 million deaths in 2013—despite the fact that hepatitis B is a vaccine-preventable disease and that hepatitis B and C are both treatable. Emerging pandemic viral infections remain a constant threat, many entering the human population from contact with animals. The most recent such infections include SARS (severe acute respiratory syndrome), MERS (Middle East respiratory syndrome), and Ebola and Zika viruses (Madhav and others 2018) as well as, perennially, influenza and chikungunya infections. Compared with antibiotics to treat bacterial infections, relatively few antiviral drugs have been developed to treat these emerging viral infections. Therefore, the most important intervention is to break the chain of transmission. A global increase in antibiotic-resistant bacteria includes a small but growing number that are resistant to most or essentially all of the available antimicrobials. Spectacular progress has been made in reducing mortality from most infectious diseases (table 1.1). For example, in low-income countries (LICs) from 2000 to 2010, the number of deaths before age 70 years from HIV/AIDS, TB, and malaria fell by 46 percent, 35 percent, and 36 percent, respectively (Norheim and others 2015). Rapid progress was also reported in other country income groups. However, table 1.1 shows also that if the death rates of 2010 remain static, about 5.1 million people will still die in 2030 from these three conditions and from other communicable diseases, many of which are concentrated in LMICs. In contrast, mortality in HICs from these conditions (except for HIV/AIDS) will be relatively small, although major pandemics of other pathogens are not predictable. Hence, infectious diseases will remain a major threat to humankind, especially in LMICs, requiring vigilance, surveillance, and new interventions of all types.

SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause disease in suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.

Visitors can play an important role in the spread of infections. Here, we incorporate an epidemic model into a game theoretical framework to investigate the effects of travel strategies on infection control. Potential visitors must decide whether to travel to a destination that is at risk of infectious disease outbreaks. We compare the individually optimal (Nash equilibrium) strategy to the group optimal strategy that maximizes the overall population utility. Economic epidemiological models often find that individual and group optimal strategies are very different. By contrast, we find perfect agreement between individual and group optimal strategies across a wide parameter regime. For more limited regimes where disagreement does occur, the disagreement is (i) generally very extreme; (ii) highly sensitive to small changes in infection transmissibility and visitor costs/benefits; and (iii) can manifest either in a higher travel volume for individual optimal than group optimal strategies, or vice versa. The simulations show qualitative agreement with the 2003 severe acute respiratory syndrome (SARS) outbreak in Beijing, China. We conclude that a conflict between individual and group optimal visitor travel strategies during outbreaks may not generally be a problem, although extreme differences could emerge suddenly under certain changes in economic and epidemiological conditions.

The aims of this study were (i) to evaluate whether routine in-feed antimicrobial use in pigs or not resulted in differences in antimicrobial resistance (AMR) E. coli at different pig producing stages, and (ii) to determine whether resistant strains were presented in pig meat postslaughter. A total of 300 commensal E. coli isolates were obtained and examined for antibiograms, AMR genes, plasmid replicons, and molecular types. The isolates were from two farms either using (A) or not using in-feed antimicrobials (NA), sampled four times during the production cycle and once postslaughter. E. coli resistant to aminoglycosides containing aadA1, aadA2, and aadB and extended-spectrum beta-lactamase-producing (ESBLP) E. coli containing blaCTX-M-1 were significantly increased in the nursery and growing periods in farm A compared to farm NA. IncI1-Iγ and IncHI2 were common in the nursery period and were shown to transfer blaCTX-M genes by conjugation. ST10 was the most common type only found in live pigs. ST604, ST877, ST1209, and ST2798 ESBLP were found only in live pigs, whereas ST72, ST302, and ST402 ESBLP were found in pig meat.

Hepatitis B virus disease progression in East Asia is most frequently associated with genotype C (HBV/C). The increasing availability of HBV/C genetic sequences and detailed annotations provides an opportunity to investigate the epidemiological factors underlying its evolutionary history. In this study, the Bayesian phylogeography framework was used to investigate the origins and patterns in spatial dissemination of HBV/C by analyzing East Asian sequences obtained from 1992 to 2010. The most recent common ancestor of HBV/C was traced back to the early 1900s in China, where it eventually diverged into two major lineages during the 1930s-1960s that gave rise to distinct epidemic waves spreading exponentially to other East Asian countries and the United States. Demographic inference of viral effective population size over time indicated similar dynamics for both lineages, characterized by exponential growth since the early 1980s, followed by a significant bottleneck in 2003 and another increase after 2004. Although additional factors cannot be ruled out, we provide evidence to suggest this bottleneck was the result of limited human movement from/to China during the SARS outbreak in 2003. This is the first extensive evolutionary study of HBV/C in East Asia as well as the first to assess more realistic spatial ecological influences between co-circulating infectious diseases. This article is protected by copyright. All rights reserved.

Human coronavirus 229E (HCoV-229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV-229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six-helix membrane-fusion structure termed the fusion core. Here, the complete fusion-core structure of HCoV-229E has been determined at 1.86 Å resolution, representing the most complete post-fusion conformation thus far among published human alphacoronavirus (α-HCoV) fusion-core structures. The overall structure of the HCoV-229E fusion core is similar to those of SARS, MERS and HCoV-NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side-by-side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α-HCoVs and β-HCoVs at certain positions and that the HCoV-229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure-based design of pan-coronavirus small molecules or peptides to inhibit viral fusion.