Analysis of DNA Sequencing Reaction Products Made with 7-Halo-7-deaza-2′-deoxyguanosine-5′-triphosphate

Abstract

7-Chloro- and 7- Iodo-7-Deaza-2′-Deoxyguanosine-5′-Triphosphates were employed as substrates replacing dGTP, dITP, or 7-Deaza-2′-Deoxyguanosine-5′-Triphosphate in sequencing reactions with Thermo Sequenase^TM. Analysis of the reaction products by denaturing gel electrophoresis indicates DNA containing these halogenated analogs can form strong secondary structures.     

Assessment of lake sturgeon (Acipenser fulvescens) recruitment in a regulated spawning tributary of Rainy Lake,Ontario

Continued study of the relationship between lake sturgeon (Acipenser fulvescens) recruitment and hydroelectric dams and operations, in a variety of river systems and habitat types is needed to improve the ability to predict and monitor impacts of the hydroelectric industry on this species. Herein, we present results of a juvenile lake sturgeon study aimed at addressing concerns over an inferred lack of recruitment resulting from spawning downstream of a hydroelectric generating station (HGS). Two years of sampling (2015 and 2016) were conducted in five sections of a 41 km long reach of the Seine River, Ontario, a lake sturgeon spawning tributary of Rainy Lake. Using an established gillnetting method, deepwater habitat was targeted to capture juvenile lake sturgeon to assess relative abundance, recruitment (cohort strength), and growth. Deepwater habitat, defined as water depths >6 m in this system, comprised only 2.1% of the wetted area in this study area. Within these habitats, a total of 331 lake sturgeon capture events were observed over the 2-years study period. The majority of the lake sturgeon catch (85%) was comprised of age-0 to age-5 individuals (both sampling years combined). Although inter-annual variation in cohort strength was apparent, each cohort between 2006 and 2016 was represented. The spatial distribution of cohorts varied among river reaches with younger individuals (age-0 and age-1) occupying reaches proximal to the Sturgeon Falls HGS, and larger, older individuals (age-2 to age-5) occupying reaches further downstream. The rarity of age-6+ individuals can likely be explained by ongoing downstream redistribution of juveniles over time, out of the Seine River and into Rainy Lake. Growth of juvenile lake sturgeon captured in the Seine River was above average relative to conspecifics from other rivers in the Hudson Bay drainage. Unfortunately, baseline data sets required to facilitate comparisons of contemporary (post-construction Sturgeon Falls HGS) versus historical (i.e. pre- Sturgeon Falls HGS) lake sturgeon recruitment, or to evaluate the influence of the Seine River Water Management Plan (2004) on lake sturgeon recruitment, are lacking. However, juvenile Lake Sturgeon are more abundant in this system than what had been surmised based on recent studies which implemented random sampling. Results indicate that juvenile lake sturgeon may reside in spawning tributaries for several years (age-0 to age-5) prior to seeking alternate habitats and highlights the value of targeted sampling (i.e. by depth) along the flow axis of rivers downstream of spawning areas when assessing lake sturgeon recruitment patterns.     

A review of the energetics of pollination biology

Pollination biology is often associated with mutualistic interactions between plants and their animal pollen vectors, with energy rewards as the foundation for co-evolution. Energy is supplied as food (often nectar from flowers) or as heat (in sun-tracking or thermogenic plants). The requirements of pollinators for these resources depend on many factors, including the costs of living, locomotion, thermoregulation and behaviour, all of which are influenced by body size. These requirements are modified by the availability of energy offered by plants and environmental conditions. Endothermic insects, birds and bats are very effective, because they move faster and are more independent of environmental temperatures, than are ectothermic insects, but they are energetically costly for the plant. The body size of endothermic pollinators appears to be influenced by opposing requirements of the animals and plants. Large body size is advantageous for endotherms to retain heat. However, plants select for small body size of endotherms, as energy costs of larger size are not matched by increases in flight speed. If high energy costs of endothermy cannot be met, birds and mammals employ daily torpor, and large insects reduce the frequency of facultative endothermy. Energy uptake can be limited by the time required to absorb the energy or eliminate the excess water that comes with it. It can also be influenced by variations in climate that determine temperature and flowering season.     

Single Sustained Inflation followed by Ventilation Leads to Rapid Cardiorespiratory Recovery but Causes Cerebral Vascular Leakage in Asphyxiated Near-Term Lambs

BackgroundA sustained inflation (SI) rapidly restores cardiac function in asphyxic, bradycardic newborns but its effects on cerebral haemodynamics and brain injury are unknown. We determined the effect of different SI strategies on carotid blood flow (CaBF) and cerebral vascular integrity in asphyxiated near-term lambs.MethodsLambs were instrumented and delivered at 139 ± 2 d gestation and asphyxia was induced by delaying ventilation onset. Lambs were randomised to receive 5 consecutive 3 s SI (multiple SI; n = 6), a single 30 s SI (single SI; n = 6) or conventional ventilation (no SI; n = 6). Ventilation continued for 30 min in all lambs while CaBF and respiratory function parameters were recorded. Brains were assessed for gross histopathology and vascular leakage.ResultsCaBF increased more rapidly and to a greater extent during a single SI (p = 0.01), which then decreased below both other groups by 10 min, due to a higher cerebral oxygen delivery (p = 0.01). Blood brain barrier disruption was increased in single SI lambs as indicated by increased numbers of blood vessel profiles with plasma protein extravasation (p = 0.001) in the cerebral cortex. There were no differences in CaBF or cerebral oxygen delivery between the multiple SI and no SI lambs.ConclusionsVentilation with an initial single 30 s SI improves circulatory recovery, but is associated with greater disruption of blood brain barrier function, which may exacerbate brain injury suffered by asphyxiated newborns. This injury may occur as a direct result of the initial SI or to the higher tidal volumes delivered during subsequent ventilation.     

Aged‐senescent cells contribute to impaired heart regeneration

Aging leads to increased cellular senescence and is associated with decreased potency of tissue‐specific stem/progenitor cells. Here, we have done an extensive analysis of cardiac progenitor cells (CPCs) isolated from human subjects with cardiovascular disease, aged 32–86 years. In aged subjects (>70 years old), over half of CPCs are senescent (p16^INK4A, SA‐β‐gal, DNA damage γH2AX, telomere length, senescence‐associated secretory phenotype [SASP]), unable to replicate, differentiate, regenerate or restore cardiac function following transplantation into the infarcted heart. SASP factors secreted by senescent CPCs renders otherwise healthy CPCs to senescence. Elimination of senescent CPCs using senolytics abrogates the SASP and its debilitative effect in vitro. Global elimination of senescent cells in aged mice (INK‐ATTAC or wild‐type mice treated with D + Q senolytics) in vivo activates resident CPCs and increased the number of small Ki67‐, EdU‐positive cardiomyocytes. Therapeutic approaches that eliminate senescent cells may alleviate cardiac deterioration with aging and restore the regenerative capacity of the heart.     

Effect of exogenous progesterone and oestradiol on plasma progesterone concentrations and follicle wave dynamics in anovulatory anoestrous post-partum dairy cattle

The effect of exogenous progesterone (P4) and of oestradiol benzoate (ODB) on plasma progesterone concentration and follicle dynamics was studied in anovulatory anoestrus (AA) post-partum pasture-fed dairy cattle. Cows (n=32) were defined AA based on not detecting a corpus luteum upon transrectal ultrasonography of the ovaries. Cows were randomly assigned to treatment with an intravaginal P4-releasing device containing 1.56 g of P4 (1Q; Cuemate, Pfizer Animal Health, Auckland, NZ; n=11) or with modified devices with double (2Q; n=11) or triple (3Q; n=10) the normal P4 dose for 8 days. Half of each group received 2 mg ODB at device insertion (Day 0) while the other half did not receive ODB at this time. All cows were treated with 1 mg ODB 1 day after intravaginal device removal (Day 9). Ultrasonography occurred daily until either ovulation or Day 15 whichever occurred sooner. Blood samples were drawn on Days 0, 1, 3, 5, 7, 8, 9, 15 and 22 for plasma P4 determination. Increasing P4 dose was associated with an increase in plasma P4 concentration during the time of device insertion (P <0.05). The highest P4 dose was associated with a delay in emergence of, but a shorter interval from emergence to maximum diameter and ovulation of, the subsequent dominant follicle (DF2) compared to the lowest P4 dose. Treatment with ODB resulted in a delay in emergence of DF2 (4.2 (0.4) versus 2.0 (0.4) days (S.E.M.) to emergence for ODB versus no-ODB; P=0.01), a smaller maximum diameter of DF2 (15.2 (0.5) versus 17.9 (0.6)mm (S.E.M.) for ODB versus no-ODB; P <0.01), a shorter interval to maximum DF2 diameter (5.0 (0.3) versus 6.8 (0.3) days (S.E.M.) for ODB versus no-ODB; P=0.03), a shorter interval from DF2 emergence to ovulation (6.3 (0.4) versus 8.5 (0.4) days (S.E.M.) for ODB versus no-ODB; P=0.02) and a tendency for a lower average plasma P4 concentration post-ovulation (i.e. average of Days 15 and 22; 2.5 (0.4) versus 3.4 (0.4) ng/ml plasma P4 for ODB versus no-ODB, respectively; P=0.08). The DF present at device insertion, was still present at device removal in three (9%) cows of which two were treated with 1Q + no-ODB and one with 3Q + ODB. It is concluded that increasing P4 dose and ODB treatment are associated with a delay in subsequent follicle wave emergence and more rapid follicle growth. Oestradiol benzoate treatment also tends to reduce the plasma P4 concentration in the subsequent luteal phase in post-partum, anoestrous dairy cattle.     

Developmental expression patterns of the signaling adapters FRS-2 and FRS-3 during early embryogenesis

Two fibroblast growth factor (FGF) receptor substrates (FRS2 and FRS3) are involved in downstream signaling from activated FGF receptors and neurotrophin-activated Trk receptors. Despite the importance of signaling from these factors in embryogenesis, FRS2 and FRS3 expression patterns during development are unknown. In this study we characterize the expression of FRS2 and FRS3 from E7 to parturition and in adult murine tissues. Both are first detected in whole E8.5 CD1 mouse embryos. FRS2 is detected as early as E7 in the developing syncytiotrophoblast, later in the neural tube (NT) and in many adult and fetal tissues. FRS3 is more restricted in location than FRS2 (fetal NT, heart, stomach, liver and some adult tissues), and is expressed predominantly in the ventricular layer of the developing NT and brains of murine embryos.     

Mathematical modelling of flow through vascular networks: implications for tumour-induced angiogenesis and chemotherapy strategies

Angiogenesis, the formation of blood vessels from a pre-existing vasculature, is a process whereby capillary sprouts are formed in response to externally supplied chemical stimuli. The sprouts then grow and develop, driven initially by endothelial cell migration, and organize themselves into a branched, connected network structure. Subsequent cell proliferation near the sprout-tip permits further extension of the capillary and ultimately completes the process. Angiogenesis occurs during embryogenesis, wound healing, arthritis and during the growth of solid tumours. In this paper we initially generate theoretical capillary networks (which are morphologically similar to those networks observed in vivo) using the discrete mathematical model of Anderson and Chaplain. This discrete model describes the formation of a capillary sprout network via endothelial cell migratory and proliferative responses to external chemical stimuli (tumour angiogenic factors, TAF) supplied by a nearby solid tumour, and also the endothelial cell interactions with the extracellular matrix. The main aim of this paper is to extend this work to examine fluid flow through these theoretical network structures. In order to achieve this we make use of flow modelling tools and techniques (specifically, flow through interconnected networks) from the field of petroleum engineering. Having modelled the flow of a basic fluid through our network, we then examine the effects of fluid viscosity, blood vessel size (i.e., diameter of the capillaries), and network structure/geometry, upon: (i) the rate of flow through the network; (ii) the amount of fluid present in the complete network at any one time; and (iii) the amount of fluid reaching the tumour. The incorporation of fluid flow through the generated vascular networks has highlighted issues that may have major implications for the study of nutrient supply to the tumour (blood/oxygen supply) and, more importantly, for the delivery of chemotherapeutic drugs to the tumour. Indeed, there are also implications for the delivery of anti-angiogenesis drugs to the network itself. Results clearly highlight the important roles played by the structure and morphology of the network, which is, in turn, linked to the size and geometry of the nearby tumour. The connectedness of the network, as measured by the number of loops formed in the network (the anastomosis density), is also found to be of primary significance. Moreover, under certain conditions, the results of our flow simulations show that an injected chemotherapy drug may bypass the tumour altogether.