Fish Gut Microbiome: Current Approaches and Future Perspectives

In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.     

To be or not to be planktonic? Self‐inhibition of biofilm development

The transition between planktonic growth and biofilm formation represents a tightly regulated developmental shift that has substantial impact on cell fate. Here, we highlight different mechanisms through which bacteria limit their own biofilm development. The mechanisms involved in these self‐inhibition processes include: (i) regulation by secreted small molecules, which govern intricate signalling cascades that eventually decrease biofilm development, (ii) extracellular polysaccharides capable of modifying the physicochemical properties of the substratum and (iii) extracellular DNA that masks an adhesive structure. These mechanisms, which rely on substances produced by the bacterium and released into the extracellular milieu, suggest regulation at the communal level. In addition, we provide specific examples of environmental cues (e.g. blue light or glucose level) that trigger a cellular response reducing biofilm development. All together, we describe a diverse array of mechanisms underlying self‐inhibition of biofilm development in different bacteria and discuss possible advantages of these processes.     

DAP5 associates with eIF2β and eIF4AI to promote Internal Ribosome Entry Site driven translation

Initiation is a highly regulated rate-limiting step of mRNA translation. During cap-dependent translation, the cap-binding protein eIF4E recruits the mRNA to the ribosome. Specific elements in the 5′UTR of some mRNAs referred to as Internal Ribosome Entry Sites (IRESes) allow direct association of the mRNA with the ribosome without the requirement for eIF4E. Cap-independent initiation permits translation of a subset of cellular and viral mRNAs under conditions wherein cap-dependent translation is inhibited, such as stress, mitosis and viral infection. DAP5 is an eIF4G homolog that has been proposed to regulate both cap-dependent and cap-independent translation. Herein, we demonstrate that DAP5 associates with eIF2β and eIF4AI to stimulate IRES-dependent translation of cellular mRNAs. In contrast, DAP5 is dispensable for cap-dependent translation. These findings provide the first mechanistic insights into the function of DAP5 as a selective regulator of cap-independent translation.     

Variations in enzyme activity in stomach and pancreatic tissue and digesta in piglets around weaning

A study was performed to investigate the effect of weaning at 4 weeks of age on the activity of digestive enzymes in the stomach and pancreatic tissue and in digesta from 3 days prior to weaning to 9 days postweaning in 64 piglets. In stomach tissue the activity of pepsin and gastric lipase was determined. Pepsin activity declined abruptly after weaning but 5 days postweaning the weaning level was regained and in the gastric contents no change in pepsin activity was observed. Weaning did not influence the activity of gastric lipase. The activity of eight enzymes and a cofactor was measured in pancreatic tissue. The effect of weaning on the enzyme activity was highly significant for all enzymes except elastase. The activity of all enzymes remained at the weaning level during day 1–2 postweaning followed by a reduction of the activity. The activity of trypsin, carboxypeptidase A, amylase and lipase exhibited minimum activity 5 days postweaning. Trypsin activity increased to the preweaning level on day 7–9 whereas the activity of the others increased but did not reach the preweaning level. The activity of chymotrypsin, carboxypeptidase B and carboxyl ester hydrolase decreased during the entire experimental period. In digesta no effect of weaning was observed on the activity of amylase and trypsin. The activity of chymotrypsin was reduced after weaning in the proximal third of the small intestine and lipase and carboxyl ester hydrolase activity was reduced in the middle and distal parts of the small intestine after weaning. The present study shows that the activities of the digestive enzymes in the pancreatic tissue are affected by weaning. Even though the pancreatic secretion cannot be judged from these results they show that the enzymes respond differently to weaning. In general the activity of the digestive enzymes in pancreatic tissue is low on day 5 postweaning which in interaction with other factors may increase the risk of developing postweaning diarrhoea.     

Expression and localization of locally produced growth factors regulating lymphangiogenesis during different stages of the estrous cycle in corpus luteum of buffalo (Bubalus bubalis)

Recent experiments using expression, immunolocalization, and cell culture approaches have provided leading insights into regulation of luteal angiogenesis by different growth factor systems and its role in the function of corpus luteum (CL) in buffalo. On the contrary, lymphangiogenesis and its regulation in the CL are still poorly understood. The aim of this study was to evaluate the expression and localization of lymphangiogenic factors (vascular endothelial growth factor [VEGF]-C and VEGFD), their receptor (VEGFR3), and lymphatic endothelial marker (LYVE1) in bubaline CL during different stages of the estrous cycle and to investigate functional role of VEGFC and VEGFD in luteal lymphangeogenesis. The mRNA and protein expression of VEGFC, VEGFD, and VEGFR3 was significantly greater in mid and late luteal phases, which correlated well with the expression of LYVE1. The lymphangiogenic factors were localized in luteal cells, exclusively in the cytoplasm. Immunoreactivity of VEGFC was greater during midluteal phase and that of VEGFD was greater during the mid and late luteal phases. Luteal cells were cultured in vitro and treated for different time duration (24, 48, and 72 hours) with VEGFC and VEGFD each at 50, 100, and 150 ng/mL concentration and VEGFC with VEGFD at 100 ng/mL concentration. The temporal increase in LYVE1 mRNA expression was significant (P < 0.05) in VEGFC and VEGFC with VEGFD treatment and no significant change was seen in VEGFD treatment. Thus, it seems likely that VEGFD itself has little role in lymphangiogenesis but along with VEGFC it might have a synergistic effect on VEGFR3 receptors for inducing lymphangiogenesis. In summary, the present study provided evidence that VEGFC and VEGFD, and their receptor VEGFR3, are expressed in bubaline CL and are localized exclusively in the cell cytoplasm, suggesting that these factors have a functional role in lymphangiogenesis of CL in buffalo.     

Molecular understandings on ‘the never thirsty’ and apomictic <Emphasis Type="Italic">Cenchrus</Emphasis> grass

The genus Cenchrus comprises around 25 species of ‘bristle clade’ grasses. Cenchrus ciliaris (buffel grass) is a hardy, perennial range grass that survives in poor sandy soils and limiting soil moisture conditions and, due to the very same reasons, this grass is one of the most prevalent fodder grasses of the arid and semi-arid regions. Most of the germplasms of Cenchrus produce seeds asexually through the process of apomeiosis. Therefore, the lack of sufficient sexual lines has hindered the crop improvement efforts in Cenchrus being confined to simple selection methods. Many attempts have been initiated in buffel grass to investigate the various molecular aspects such as genomic signatures of different species and genotypes, molecular basis of abiotic stress tolerance and reproductive performance. Even though it is an important fodder crop, molecular investigations in Cenchrus lack focus and the molecular information available on this grass is scanty. Cenchrus is a very good gene source for abiotic stress tolerance and apomixis studies. Biotechnological interventions in Cenchrus can help in crop improvement in Cenchrus as well as other crops through transgenic technology or marker assisted selection. To date no consolidated review on biotechnological interventions in Cenchrus grass has been published. Therefore we provide a thorough and in depth review on molecular research in Cenchrus focusing on molecular signatures of evolution, tolerance to abiotic stress and apomictic reproductive mechanism.     

Isolation and characterization of brassinosteroids from immature seeds of Camellia sinensis (O) Kuntze

Brassinosteroids play an important role in growth and development of plants. They have been reported universally in all the plants. The present study deals with the presence of these compounds in immature tea seeds. Five brassinosteroids, i.e. 6-deoxo-28-norcathasterone, 6-deoxo-28-norteasterone, 3-dehydro-6-deoxo-28-norteasterone, 6-deoxo-28-nortyphasterol and 6-deoxo-28-norcastasterone have been isolated and identified by GC–MS. The identified brassinosteroids and their derivatives are active constituents of late C-6 oxidation pathway, thereby suggesting the biosynthesis of brassinosteroids in tea seeds by late C-6 oxidation pathway.     

Deformed Wing Virus Implicated in Overwintering Honeybee Colony Losses

The worldwide decline in honeybee colonies during the past 50 years has often been linked to the spread of the parasitic mite Varroa destructor and its interaction with certain honeybee viruses. Recently in the United States, dramatic honeybee losses (colony collapse disorder) have been reported; however, there remains no clear explanation for these colony losses, with parasitic mites, viruses, bacteria, and fungal diseases all being proposed as possible candidates. Common characteristics that most failing colonies share is a lack of overt disease symptoms and the disappearance of workers from what appears to be normally functioning colonies. In this study, we used quantitative PCR to monitor the presence of three honeybee viruses, deformed wing virus (DWV), acute bee paralysis virus (ABPV), and black queen cell virus (BQCV), during a 1-year period in 15 asymptomatic, varroa mite-positive honeybee colonies in Southern England, and 3 asymptomatic colonies confirmed to be varroa mite free. All colonies with varroa mites underwent control treatments to ensure that mite populations remained low throughout the study. Despite this, multiple virus infections were detected, yet a significant correlation was observed only between DWV viral load and overwintering colony losses. The long-held view has been that DWV is relatively harmless to the overall health status of honeybee colonies unless it is in association with severe varroa mite infestations. Our findings suggest that DWV can potentially act independently of varroa mites to bring about colony losses. Therefore, DWV may be a major factor in overwintering colony losses.Deformed wing virus (DWV), acute bee paralysis virus (ABPV), and black queen cell virus (BQCV) are single-stranded positive-sense RNA viruses of the order Picornavirales and are regularly detected in honeybee populations in the United Kingdom (1). ABPV has been assigned to the family Dicistroviridae and is known to follow a classic acute-type infection strategy since relatively low loads (10³ to 10⁶ viruses per honeybee) can rapidly translate into overt symptoms of paralysis and ultimately death for the honeybee, depending on the mode of transmission (6, 33). ABPV shares >92% sequence homology with other members of the family Dicistroviridae, Kashmir bee virus and Israeli acute paralysis virus, across the eight conserved domains of the RNA-dependent RNA polymerase gene, and it has been proposed that these viruses have recently diverged and are variants of each other (7). Advances in the study of this proposed ABPV complex is revealing the significant impact these viruses may have on honeybee colonies on a global scale. For example, a recent study in the United States has observed a correlation between Israeli acute paralysis virus and colony collapse disorder (17). That said, other agents, including bacteria and microsporidia, have also been proposed as important factors in the onset of colony loss (25, 27).BQCV is similar to ABPV in that it, too, follows a typical acute infection strategy. This virus is known to infect honeybee queen cell larvae, causing the larvae to discolor and die (5). It has been shown to be associated with the microsporidian Nosema apis (4) although whether N. apis has a direct role in the transmission of this virus still needs to be determined. Both ABPV and BQCV have been detected in worker honeybees and pupae (38), and the viruses are transmitted orally, via food and feeding activities (14). BQCV has also been detected in queen honeybees (13), suggesting that vertical transmission is also important for this virus. Both BQCV (12) and ABPV (38) have been detected within the varroa mite; however, only ABPV (9) has been shown to be vectored by varroa mites and has been found associated with dead colonies infested with varroa mites in Germany, Russia, and the United States (1). Later modeling work (33) indicated that very large (10,000+) mite populations are required to kill a colony since it is difficult for ABPV to become established among the bee population due to its high virulence.DWV is currently designated as a member of the unassigned genus Iflavirus within the order Picornavirales. It is generally considered as less virulent than ABPV or Kashmir bee virus, but it is known to cause overt symptoms of wing deformities in developing honeybees, resulting in emerging honeybees that are unable to fly and die shortly (5). It is also speculated that a cloud of DWV sequence variants exists that have evolved from a common ancestor. This is due to the high sequence similarities DWV isolates share with Kakugo virus and Varroa destructor virus within the RNA-dependent RNA polymerase gene, yet differences in virus epidemiology and pathological effects distinguish them from each other (29). DWV has been detected in worker honeybees, pupae, larvae, drones, and queens (15, 18, 20) as well as within the varroa mite (38, 43) and more recently the mite Tropilaelaps mercedesae (21), implying a range of horizontal and vertical transmission routes. Despite their global occurrence, it is generally accepted that DWVs play a secondary role in the causes of honeybee disease compared to their parasitic and bacterial counterparts as the viruses routinely reside at low levels in colonies, with symptomatic infections being rare (5). Moreover, multiple variants with differing infection strategies can account for a lack of discernible symptoms.Whether these viruses follow a persistent, latent, inapparent, or progressive infection strategy still remains unclear. Persistent (often called chronic) infections imply that the rate of infection within a host is in balance with the reproduction rate of the infected cell type or host itself. This is achieved through a combination of changing virus replication and host immune responses. Latent infections occur when the virus lies dormant within the host (replication inactive) until activation by defined stimuli. Progressive infections are caused by viruses that enter the host cell and replicate undetected for many cellular generations over many years before manifesting overt or acute symptoms. These three infection strategies all evade the host immune system, which results in the inability of the host to fully expel the virus, and this inability is often lethal. Inapparent (often referred to as covert) infections are indicative of a highly evolved relationship between the virus and natural host. Moreover, these infections are distinct in that the natural host can eventually clear itself from this short-term infection (19). Infections of DWV are often described as inapparent (15); however, Yue et al. (44) have suggested that a distinction should be made between “true inapparent” and their newly defined “covert infection” based on the long-term nature of DWV infection in honeybee colonies and on the nature of its transmission. This conclusion is congruent with current knowledge that traditional serological screening methods for DWV have limitations in their sensitivity (20). Therefore, the presence and duration of DWV within colonies have often been underestimated using serological assays as the overt symptoms of the deformed wing phenotype (>10¹¹ virions per honeybee) are short-lived. Advances in virus detection methodologies have enabled the development of more sensitive techniques, such as PCR, and this has demonstrated that DWV persists for longer periods within colonies (38). However, based on the current research evidence, a case could be made that DWV actually follows the classic persistent infection strategy.DWV is thought to have an intricate relationship with varroa mites such that immunosuppression of the honeybee pupae by the mites results in increased DWV amplification when the honeybees are exposed to other pathogens (42). It has additionally been shown that the number of mites parasitizing honeybee pupae is positively correlated with the probability of their developing malformed wings (10). Other findings indicate that DWV replication within the mite and subsequent transmission to developing honeybees lead to the increased likelihood of the bees'' emerging with wing deformities (24, 43). Taken together, the expectation is that DWV-associated colony collapse would typically occur in the presence of a large (>2,000) varroa mite infestation carrying high levels of DWV and with a high proportion of deformed honeybees. While the effect of varroa mite-induced DWV disease is well recognized, i.e., wing deformities coupled with downregulation of immunity-related genes and antimicrobial peptides (36, 42) and impaired learning behavior (28), the impact of non-varroa mite-vectored DWV within asymptomatic honeybees still needs to be realized. Moreover, it was recently reported that varroa mite-free bumblebees that tested positive for DWV actually showed symptoms of DWV infection (23). Even though these bumblebees were in close proximity to DWV-infected and varroa mite-infested honeybee colonies, it is evidence that the dependency of DWV on varroa mite vectoring for a symptomatic infection (manifested as classic wing deformities or other symptoms) may not be as critical as previously thought.The purpose of this study was to investigate asymptomatic viral dynamics within husbanded honeybee colonies over an annual cycle. We set out to observe the relationship, if any, between virus infections, varroa mite parasitism and vectoring, honeybee colony health, and colony longevity. For the first time, a quantitative analysis of three picorna-like honeybee viruses over the course of a year was undertaken for DWV, ABPV, and BQCV.     

The ITGAV rs3738919 variant and susceptibility to rheumatoid arthritis in four Caucasian sample sets

Introduction

Angiogenesis is an important process in the development of destructive synovial pannus in rheumatoid arthritis (RA). The ITGAV +gene encodes a cell cycle-associated antigen, integrin ανβ 3, which plays a role in RA angiogenesis. Previously, two independent studies identified an association between the major allele of the ITGAV single-nucleotide polymorphism (SNP) rs3738919 and RA. We therefore tested this association in an independent study using New Zealand (NZ) and Oxford (UK) RA case control samples.

Methods

We compared genotype frequencies in 740 NZ Caucasian RA patients and 553 controls genotyped for rs3738919, using a polymerase chain reaction-restriction fragment length polymorphism assay. A TaqMan genotyping SNP assay was used to type 713 Caucasian RA patients and 515 control samples from Oxford for the rs3738919 variant. Association of rs3738919 with RA was tested in these two sample sets using the chi-square goodness-of-fit test. The Mantel-Haenszel test was used to perform a meta-analysis, combining the genetic results from four independent Caucasian case control cohorts, consisting of 3,527 cases and 4,126 controls. Haplotype analysis was also performed using SNPs rs3911238, rs10174098 and rs3738919 in the Wellcome Trust Case Control Consortium, NZ and Oxford case control samples.

Results

We found no evidence for association between ITGAV and RA in either the NZ or Oxford sample set (odds ratio [OR] = 0.88, P_allelic = 0.11 and OR = 1.18, P_allelic = 0.07, respectively). Inclusion of these data in a meta-analysis (random effects) of four independent cohorts (3,527 cases and 4,126 controls) weakens support for the hypothesis that rs3738919 plays a role in the development of RA (OR_combined = 0.92, 95% confidence interval 0.80 to 1.07; P = 0.29). No consistent haplotype associations were evident.

Conclusions

Association of ITGAV SNP rs7378919 with RA was not replicated in NZ or Oxford case control sample sets. Meta-analysis of these and previously published data lends limited support for a role for the ITGAV in RA in Caucasians of European ancestry.