Patterns of sequence variation in the mitochondrial D-loop region of shrews

Direct sequencing of the mitochondrial displacement loop (D-loop) of shrews (genus Sorex) for the region between the tRNA(Pro) and the conserved sequence block-F revealed variable numbers of 79-bp tandem repeats. These repeats were found in all 19 individuals sequenced, representing three subspecies and one closely related species of the masked shrew group (Sorex cinereus cinereus, S. c. miscix, S. c. acadicus, and S. haydeni) and an outgroup, the pygmy shrew (S. hoyi). Each specimen also possessed an adjacent 76-bp imperfect copy of the tandem repeats. One individual was heteroplasmic for length variants consisting of five and seven copies of the 79-bp tandem repeat. The sequence of the repeats is conducive to the formation of secondary structure. A termination-associated sequence is present in each of the repeats and in a unique sequence region 5' to the tandem array as well. Mean genetic distance between the masked shrew taxa and the pygmy shrew was calculated separately for the unique sequence region, one of the tandem repeats, the imperfect repeat, and these three regions combined. The unique sequence region evolved more rapidly than the tandem repeats or the imperfect repeat. The small genetic distance between pairs of tandem repeats within an individual is consistent with a model of concerted evolution. Repeats are apparently duplicated and lost at a high rate, which tends to homogenize the tandem array. The rate of D- loop sequence divergence between the masked and pygmy shrews is estimated to be 15%-20%/Myr, the highest rate observed in D-loops of mammals. Rapid sequence evolution in shrews may be due either to their high metabolic rate and short generation time or to the presence of variable numbers of tandem repeats.      

The functional roles of species in metacommunities,as revealed by metanetwork analyses of bird–plant frugivory networks

Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird–plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird–plant interactions involving birds feeding only on‐the‐tree or both on and under‐the‐tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under‐the‐tree. Moreover, bird–plant interactions associated with large‐seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on‐the‐tree and shared birds contributed more to metanetwork organisation whereas under‐the‐tree birds were more involved in local processes. We would expect that species’ roles in the metanetwork will translate into different conservation values for maintaining functioning of seed‐dispersal networks.     

Localized Hotspots Drive Continental Geography of Abnormal Amphibians on U.S. Wildlife Refuges

Amphibians with missing, misshapen, and extra limbs have garnered public and scientific attention for two decades, yet the extent of the phenomenon remains poorly understood. Despite progress in identifying the causes of abnormalities in some regions, a lack of knowledge about their broader spatial distribution and temporal dynamics has hindered efforts to understand their implications for amphibian population declines and environmental quality. To address this data gap, we conducted a nationwide, 10-year assessment of 62,947 amphibians on U.S. National Wildlife Refuges. Analysis of a core dataset of 48,081 individuals revealed that consistent with expected background frequencies, an average of 2% were abnormal, but abnormalities exhibited marked spatial variation with a maximum prevalence of 40%. Variance partitioning analysis demonstrated that factors associated with space (rather than species or year sampled) captured 97% of the variation in abnormalities, and the amount of partitioned variance decreased with increasing spatial scale (from site to refuge to region). Consistent with this, abnormalities occurred in local to regional hotspots, clustering at scales of tens to hundreds of kilometers. We detected such hotspot clusters of high-abnormality sites in the Mississippi River Valley, California, and Alaska. Abnormality frequency was more variable within than outside of hotspot clusters. This is consistent with dynamic phenomena such as disturbance or natural enemies (pathogens or predators), whereas similarity of abnormality frequencies at scales of tens to hundreds of kilometers suggests involvement of factors that are spatially consistent at a regional scale. Our characterization of the spatial and temporal variation inherent in continent-wide amphibian abnormalities demonstrates the disproportionate contribution of local factors in predicting hotspots, and the episodic nature of their occurrence.     

Modeling interactions between voltage-gated Ca2+ channels and KCa1.1 channels

High voltage-activated (HVA) Cav channels form complexes with KCa1.1 channels, allowing reliable activation of KCa1.1 current through a nanodomain interaction. We recently found that low voltage-activated Cav3 calcium channels also create KCa1.1-Cav3 complexes. While coimmunoprecipitation studies again supported a nanodomain interaction, the sensitivity to calcium chelating agents was instead consistent with a microdomain interaction. A computational model of the KCa1.1-Cav3 complex suggested that multiple Cav3 channels were necessary to activate KCa1.1 channels, potentially causing the KCa1.1-Cav3 complex to be more susceptible to calcium chelators. Here, we expanded the model and compared it to a KCa1.1-Cav2.2 model to examine the role of Cav channel conductance and kinetics on KCa1.1 activation. As found for direct recordings, the voltage-dependent and kinetic properties of Cav3 channels were reflected in the activation of KCa1.1 current, including transient activation from lower voltages than other KCa1.1-Cav complexes. Substantial activation of KCa1.1 channels required the concerted activity of several Cav3.2 channels. Combined with the effect of EGTA, these results suggest that the Ca²⁺ domains of several KCa1.1-Cav3 complexes need to cooperate to generate sufficient [Ca²⁺]_i, despite the physical association between KCa1.1 and Cav3 channels. By comparison, Cav2.2 channels were twice as effective at activating KCa1.1 channels and a single KCa1.1-Cav2.2 complex would be self-sufficient. However, even though Cav3 channels generate small, transient currents, the regulation of KCa1.1 activity by Cav3 channels is possible if multiple complexes cooperate through microdomain interactions.     

Behaviour and Ecology of the Chough and the Alpine Chough

Analysis of Nest Record Cards reveals altitudinal and habitat differencesbetween these two species. The resident or partially migratory Stonechat has a longer breeding season (with a potential for rearing three broods) than the Whinchat which is a trans-Saharan migrant and arrives later. It is suggested that the greater productivity of the Stonechat might counterbalance a higher winter mortality.     

The influence of reproductive phase on lipopolysaccharide stimulation of prostacyclin production and cyclooxygenase-2 protein concentrations in reproductive and systemic arteries of the sheep

Cyclooxygenase, the enzyme that converts arachidonate to prostaglandins, plays a regulatory role in vasodilation under normal and pathological conditions. Studies were conducted to determine the effects of reproductive phase and lipopolysaccharide (LPS) on production of PGI2 and amounts of cyclooxygenase protein in uterine, mammary, mesenteric, and renal arteries. Arteries were collected from ewes during the follicular (Day 0 = estrus) or luteal (Day 10) phase of the estrous cycle and were cultured in the presence of LPS. After 24 h, media were collected and analyzed for 6-keto-PGF1alpha, the stable metabolite of PGI2. In addition, arteries were collected and homogenized and the relative concentration of cyclooxygenase was determined via Western analysis. Lipopolysaccharide stimulated PGI2 production in all four-artery types from both follicular and luteal phase ewes (p < 0.001). Upon LPS stimulation, uterine and mammary arteries produced more PGI2 compared to mesenteric and renal arteries (p = 0.04). The phase of estrous cycle did not affect PGI2 production by any of the artery populations exposed to LPS (p = 0.35). There was no cyclooxygenase-2 in untreated uterine and mammary arteries and no cyclooxygenase-2 was detected in untreated or LPS-treated mesenteric and renal arteries. In contrast, LPS-treated uterine and mammary arteries from luteal phase ewes had higher (p = 0.064) cyclooxygenase-2 concentrations than those from follicular phase ewes. These results suggest that the hormone conditions of the follicular (high estrogen) and luteal (high progesterone) phases of the ovarian cycle play a role in regulating uterine and mammary artery but not mesenteric and renal artery response to LPS.     

Calcium dynamics during fertilization in C. elegans

Background

Of the animals typically used to study fertilization-induced calcium dynamics, none is as accessible to genetics and molecular biology as the model organism Caenorhabditis elegans. Motivated by the experimental possibilities inherent in using such a well-established model organism, we have characterized fertilization-induced calcium dynamics in C. elegans.

Results

Owing to the transparency of the nematode, we have been able to study the calcium signal in C. elegans fertilization in vivo by monitoring the fluorescence of calcium indicator dyes that we introduce into the cytosol of oocytes. In C. elegans, fertilization induces a single calcium transient that is initiated soon after oocyte entry into the spermatheca, the compartment that contains sperm. Therefore, it is likely that the calcium transient is initiated by contact with sperm. This calcium elevation spreads throughout the oocyte, and decays monotonically after which the cytosolic calcium concentration returns to that preceding fertilization. Only this single calcium transient is observed.

Conclusion

Development of a technique to study fertilization induced calcium transients opens several experimental possibilities, e.g., identification of the signaling events intervening sperm binding and calcium elevation, identifying the possible roles of the calcium elevation such as the completion of meiosis, the formation of the eggshell, and the establishing of the embryo's axis of symmetry.     

Association between blood plasma urea nitrogen levels and reproductive fluid urea nitrogen and ammonia concentrations in early lactation dairy cows

Two experiments were conducted to study the relationship of blood plasma urea nitrogen (PUN) concentrations with NH3, urea nitrogen, K, Mg, P, Ca, and Na concentrations in fluid of preovulatory follicles (experiment 1) and the relationships of PUN concentration and stage of estrus cycle with ammonia and urea nitrogen concentrations in uterine fluids (experiment 2) in early lactation dairy cows. Mean PUN levels were used to distribute cows into two groups: cows with PUN>or=20 mg/dl (HPUN), and cows with PUN<20 mg/dl (LPUN). In experiment 1, blood and follicular fluids from preovulatory follicles of 38 early lactation dairy cows were collected on the day of estrus (day 0) 4h after feed was offered. Follicular fluid NH3 was higher (P<0.01) in HPUN cows (339.0 micromol/L+/-72.2) compared to LPUN cows (93.9 micromol/L+/-13.1). Follicular fluid urea N was higher (P<0.001) in HPUN cows (22.4 mg/dl+/-0.4) compared to LPUN cows (17.0 mg/dl+/-0.3). PUN and follicular fluid urea N were correlated (r2=0.86) within cows. In experiment 2, blood and uterine fluids were collected from 30 cows on day 0 and on day 7. Uterine fluid NH3 was higher (P=0.05) in HPUN cows (1562 micromol/L+/-202) than in LPUN cows (1082 micromol/L+/-202) on day 7, but not on day 0. Uterine fluid urea N was higher (P<0.001) in HPUN cows than in LPUN cows on day 0 (26.9 mg/dl+/-1.3 and 20.4 mg/dl+/-0.7) and day 7 (26.5 mg/dl+/-1.1 and 21.4 mg/dl+/-1.1). There was a correlation (r2=0.17) between PUN and uterine fluid urea N within cows. The results of this study indicate that high PUN concentrations were associated with elevated NH3 and urea N concentrations in the preovulatory follicular fluids on the day of estrus and in the uterine fluid during the luteal phase of the estrous cycle in early lactation dairy cows. Elevated NH3 or urea N concentrations in the reproductive fluids may contribute to reproductive inefficiency in dairy cows with elevated plasma urea nitrogen due to embryo toxicity.     

Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase

The requirement for d-alanine in the peptidoglycan layer of bacterial cell walls is fulfilled in part by alanine racemase (EC 5.1.1.1), a pyridoxal 5'-phosphate (PLP)-assisted enzyme. The enzyme utilizes two antiparallel bases focused at the C(alpha) position and oriented perpendicular to the PLP ring to facilitate the equilibration of alanine enantiomers. Understanding how this two-base system is utilized and controlled to yield reaction specificity is therefore a potential means for designing antibiotics. Cycloserine is a known alanine racemase suicide substrate, although its mechanism of inactivation is based on transaminase chemistry. Here we characterize the effects of a Y265F mutant (Tyr265 acts as the catalytic base in the l-isomer case) of Bacillus stearothermophilus alanine racemase on cycloserine inactivation. The Y265F mutant reduces racemization activity 1600-fold [Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. (1999) J. Biochem. 126, 781-786] and only leads to formation of the isoxazole end product (the result of the transaminase pathway) in the case of d-cycloserine, in contrast to results obtained using the wild-type enzyme. l-Cycloserine, on the other hand, utilizes a number of alternative pathways in the absence of Y265, emphasizing the importance of Y265 in both the inactivation and racemization pathway. In combination with the kinetics of inactivation, these results suggest roles for each of the two catalytic bases in racemization and inactivation, as well as the importance of Y265 in "steering" the chemistry to favor one pathway over another.     

Structural insights into the mechanism of PEPCK catalysis

Phosphoenolpyruvate carboxykinase catalyzes the reversible decarboxylation of oxaloacetic acid with the concomitant transfer of the gamma-phosphate of GTP to form PEP and GDP as the first committed step of gluconeogenesis and glyceroneogenesis. The three structures of the mitochondrial isoform of PEPCK reported are complexed with Mn2+, Mn2+-PEP, or Mn2+-malonate-Mn2+ GDP and provide the first observations of the structure of the mitochondrial isoform and insight into the mechanism of catalysis mediated by this enzyme. The structures show the involvement of the hyper-reactive cysteine (C307) in the coordination of the active site Mn2+. Upon formation of the PEPCK-Mn2+-PEP or PEPCK-Mn2+-malonate-Mn2+ GDP complexes, C307 coordination is lost as the P-loop in which it resides adopts a different conformation. The structures suggest that stabilization of the cysteine-coordinated metal geometry holds the enzyme as a catalytically incompetent metal complex and may represent a previously unappreciated mechanism of regulation. A third conformation of the mobile P-loop in the PEPCK-Mn2+-malonate-Mn2+ GDP complex demonstrates the participation of a previously unrecognized, conserved serine residue (S305) in mediating phosphoryl transfer. The ordering of the mobile active site lid in the PEPCK-Mn2+-malonate-Mn2+ GDP complex yields the first observation of this structural feature and provides additional insight into the mechanism of phosphoryl transfer.