Parallel detection of ancient pathogens via array-based DNA capture

DNA capture coupled with next generation sequencing is highly suitable for the study of ancient pathogens. Screening for pathogens can, however, be meticulous when assays are restricted to the enrichment of single organisms, which is common practice. Here, we report on an array-based DNA capture screening technique for the parallel detection of nearly 100 pathogens that could have potentially left behind molecular signatures in preserved ancient tissues. We demonstrate the sensitivity of our method through evaluation of its performance with a library known to harbour ancient Mycobacterium leprae DNA. This rapid and economical technique will be highly useful for the identification of historical diseases that are difficult to characterize based on archaeological information alone.     

Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent,Treponema pallidum

The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.     

Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes

Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.     

Effect of the first GnRH and two doses of PGF2α in a 5-day progesterone-based CO-Synch protocol on heifer pregnancy

The objectives were (1) to determine the effects of gonadorelin hydrochloride (GnRH) injection at controlled internal drug release (CIDR) insertion on Day 0 and the number of PGF2α doses at CIDR removal on Day 5 in a 5-day CO-Synch + CIDR program on pregnancy rate (PR) to artificial insemination (AI) in heifers; (2) to examine how the effect of systemic concentration of progesterone and size of follicles influenced treatment outcome. Angus cross beef heifers (n = 1018) at eight locations and Holstein dairy heifers (n = 1137) at 15 locations were included in this study. On Day 0, heifers were body condition scored (BCS), and received a CIDR. Within farms, heifers were randomly divided into two groups: at the time of CIDR insertion, the GnRH group received 100 μg of GnRH and No-GnRH group received none. On Day 5, all heifers received 25 mg of PGF2α at the time of CIDR insert removal. The GnRH and No-GnRH groups were further divided into 1PGF and 2PGF groups. The heifers in 2PGF group received a second dose of PGF2α 6 hours after the administration of the first dose. Beef heifers underwent AI at 56 hours and dairy heifers at 72 hours after CIDR removal and received 100 μg of GnRH at the time of AI. Pregnancy was determined approximately at 35 and/or 70 days after AI. Controlling for herd effect (P < 0.06), the treatments had significant effect on AI pregnancy in beef heifers (P = 0.03). The AI-PRs were 50.3%, 50.2%, 59.7%, and 58.3% for No-GnRH + PGF + GnRH, No-GnRH + 2PGF + GnRH, GnRH + PGF + GnRH, and GnRH + 2PGF + GnRH groups, respectively. The AI-PRs were ranged from 50% to 62.4% between herds. Controlling for herd effects (P < 0.01) and for BCS (P < 0.05), the AI pregnancy was not different among the treatment groups in dairy heifers (P > 0.05). The AI-PRs were 51.2%, 51.9%, 53.9%, and 54.5% for No-GnRH + PGF + GnRH, No-GnRH + 2PGF + GnRH, GnRH + PGF + GnRH, and GnRH + 2PGF + GnRH groups, respectively. The AI-PR varied among locations from 48.3% to 75.0%. The AI-PR was 43.5%, 50.4%, and 64.2% for 2.5 or less, 2.75 to 3.5, and greater than 3.5 BCS categories. Numerically higher AI-PRs were observed in beef and dairy heifers that exhibited high progesterone concentrations at the time of CIDR insertion (>1 ng/mL, with a CL). In addition, numerically higher AI-PRs were also observed in heifers receiving CIDR + GnRH with both high and low progesterone concentration (<1 ng/mL) initially compared with heifers receiving a CIDR only with low progesterone. In dairy heifers, there were no differences in the pregnancy loss between 35 and 70 days post-AI among the treatment groups (P > 0.1). In conclusion, GnRH administration at the time of CIDR insertion is advantageous in beef heifers, but not in dairy heifers, to improve AI-PR in the 5-day CIDR + CO-Synch protocol. In addition, in this study, both dairy heifers that received either one or two PGF2α doses at CIDR removal resulted in similar AI-PR in this study regardless of whether they received GnRH at CIDR insertion.     

Effect of intrauterine administration of gonadotropin releasing hormone on serum LH concentrations in lactating dairy cows

The objectives were to compare: (1) preovulatory serum LH concentrations, and (2) synchronization of ovulation, after im or iu administration of the second GnRH treatment of Ovsynch in lactating dairy cows. Lactating cows (N = 23) were presynchronized with two injections of PGF_2α given 14 days apart (starting at 34 ± 3 days in milk), followed by Ovsynch (GnRH-7 d-PGF_2α-56 h-GnRH) 12 days later. At the time of the second GnRH of Ovsynch (Hour 0), cows were blocked by parity and randomly assigned to 1 of 3 groups: (1) control group (CON; N = 7) were given 2 mL sterile water im; (2) intramuscular group (IM; N = 8) received 100 μg of GnRH im; and (3) intrauterine group (IU; N = 8) had 100 μg GnRH infused in the uterus (2 mL). Blood samples for serum LH concentrations were collected at Hours 0, 0.5, 1, 1.5, 2, 3, and 4. Furthermore, ultrasonography was performed twice daily (12-h intervals) from Hours 0 to 60 to confirm ovulation. The LH concentrations were greater (P < 0.05) in the IM than IU and CON groups at Hours 0, 0.5, 1, 1.5, 2, 3, and 4. Although LH concentrations were numerically higher in the IU group, LH concentrations within the IU and CON groups did not change over time. More cows ovulated in the IM (8/8) and IU (7/8) groups within 60 h after the second GnRH administration compared with the CON (2/7) group. In summary, serum LH concentrations were lower in the IU versus IM group, but the proportion of cows that ovulated within 60 h was similar between these two groups. Therefore, iu administration of GnRH may be an alternative route of delivery to synchronize ovulation in beef and dairy cattle.     

Structural basis of N‐end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS

In Escherichia coli, the ClpAP protease, together with the adaptor protein ClpS, is responsible for the degradation of proteins bearing an amino‐terminal destabilizing amino acid (N‐degron). Here, we determined the three‐dimensional structures of ClpS in complex with three peptides, each having a different destabilizing residue—Leu, Phe or Trp—at its N terminus. All peptides, regardless of the identity of their N‐terminal residue, are bound in a surface pocket on ClpS in a stereo‐specific manner. Several highly conserved residues in this binding pocket interact directly with the backbone of the N‐degron peptide and hence are crucial for the binding of all N‐degrons. By contrast, two hydrophobic residues define the volume of the binding pocket and influence the specificity of ClpS. Taken together, our data suggest that ClpS has been optimized for the binding and delivery of N‐degrons containing an N‐terminal Phe or Leu.     

Spatial and Temporal Changes in Testis Morphology and Sperm Ultrastructure of the Sportfish Sauger (Sander canadensis)

The objective of this study was to assess testicular morphology and spermatozoal structure spatially within the reproductive tract and temporally among seasons in the sauger (Sander canadensis). The testis exists as two separate lobes joined at the urogenital pore and were characterised as unrestricted lobular with seminiferous tubules terminating at the ventral periphery and coalescing dorsally on the main sperm duct. Differences were observed between the pre-breeding season (November) and breeding season (March), with every stage of spermatogenesis occurring in spermatocysts in pre-breeding season in contrast to only spermatozoa being present in the tubules and main duct during the breeding season. Longitudinal folds in the main duct epithelium increased in number with increasing proximity to the urogenital pore, greatly increasing epithelial height regardless of season. Sauger spermatozoa consisted of an ovoid head, a midpiece containing 2 – 4 mitochondria incorporated into the head and a single flagellum containing an asymmetrical lateral ribbon. Motile spermatozoa were found throughout the testis during the breeding season. A decrease in sperm concentration was quantified moving proximally, suggesting a hydration effect by the main duct epithelium during the breeding season. These observations fill an important knowledge gap regarding reproductive biology of this impactful recreational fish species.     

Effects of administration of ergotamine tartrate on fertility of yearling beef bulls

Sixteen yearling bulls were utilized to investigate administration of ergotamine tartrate on semen parameters, fertilization, and endocrinology. Bulls were allotted to a control diet of cracked corn, corn silage, and soybean meal (CON, n = 8) or a diet supplemented daily with 40 microg/kg body weight of ergotamine tartrate (ET, n = 8). Blood samples, average daily gain, scrotal circumference and rectal temperatures were collected every 14 day. Semen samples were obtained every 60 day and evaluated for motility and morphology. Scrotal temperatures were obtained by thermography immediately before electroejaculation. Semen from a subset of bulls from each treatment was also evaluated for in vitro fertilization. Administration of ET increased rectal temperature and resulted in lower scrotal temperatures compared to CON bulls (P < 0.05). However, prolactin, scrotal circumference, testosterone, and semen motility and morphology did not differ between groups throughout the experimental period (224 day). Cleavage rates of embryos derived from in vitro fertilization (IVF) with semen of bulls, fed with ET, were reduced compared to CON (P < 0.05); however, development of cleaved embryos to blastocyst did not differ between treatments. In conclusion, extended exposure of bulls to ET appeared to reduce fertilization potential of sperm.     

Drosophila doubletime mutations which either shorten or lengthen the period of circadian rhythms decrease the protein kinase activity of casein kinase I

In both mammals and fruit flies, casein kinase I has been shown to regulate the circadian phosphorylation of the period protein (PER). This phosphorylation regulates the timing of PER's nuclear accumulation and decline, and it is necessary for the generation of circadian rhythms. In Drosophila melanogaster, mutations affecting a casein kinase I (CKI) ortholog called doubletime (dbt) can produce short or long periods. The effects of both a short-period (dbt(S)) and long-period (dbt(L)) mutation on DBT expression and biochemistry were analyzed. Immunoblot analysis of DBT in fly heads showed that both the dbt(S) and dbt(L) mutants express DBT at constant levels throughout the day. Glutathione S-transferase pull-down assays and coimmunoprecipitation of DBT and PER showed that wild-type DBT, DBT(S), and DBT(L) proteins can bind to PER equivalently and that these interactions are mediated by the evolutionarily conserved N-terminal part of DBT. However, both the dbt(S) and dbt(L) mutations reduced the CKI-7-sensitive kinase activity of an orthologous Xenopus laevis CKIdelta expressed in Escherichia coli. Moreover, expression of DBT in Drosophila S2 cells produced a CKI-7-sensitive kinase activity which was reduced by both the dbt(S) and dbt(L) mutations. Thus, lowered enzyme activity is associated with both short-period and long-period phenotypes.