The microbial world is a rich tapestry of communities experienced at the micron scale, but often studied at the macro scale. The methods commonly used to study microbial communities are unable to capture this heterogeneity, limiting insight into the processes that create them. High resolution methods have been applied to the human gut, but not at sufficient scale to sufficiently characterize the spatial structure of the community. Here, we examine the methods we use to study microbial communities, their limitations, and present SAMPL-seq, a method that allows for micron-scale interrogation of human and murine gut communities. In this we discover novel and consistent colocalization of microbial taxa across people. Further, we use many of the methods discussed to explore spatial heterogeneity of the microbes of hospital rooms and fusobacterial strains in the gut, revealing before unseen natural diversity.

No description available.

The lactational strategy of <u>Thrichomys apereoides</u>, a tropical hystricomorph rodent was examined. Milk composition and yield, and mammary gland composition was determined. / Master of Science

This study was designed to investigate the effects of dietary intake of sugars as well as type 2 diabetes (T2D) on mesenteric arterial function in rats with respect to sex. To test the effects of simple sugars, Sprague-Dawley female rats were supplemented with 20% w/v glucose or fructose in drinking water for 8 weeks. To study the effects of T2D and sex, two diabetic rat models were used- Zucker Diabetic Fatty (ZDF) (an established monogenic model of T2D) and UC Davis Type 2 Diabetes Mellitus (UCD-T2DM, (a novel and validated polygenic model of T2D). The plasma analytes for metabolic parameters and mesenteric arterial responses to vasodilator and vasoconstrictor agents were determined. The expression of molecules associated with vascular response (eg. endothelial nitric oxide (NO) synthase (eNOS) and small conductance calcium-dependent potassium channels (SKCa)) were also evaluated in mesenteric arterial tissues. The main objectives of the study were whether 1) the mesenteric arterial function was impaired in sugar-supplemented and diabetic rats, 2) sex differences exist in the development of abnormal vascular responses, and 3) there were changes in the relative contributions of endothelium-derived relaxing factors (EDRFs) in modulating vascular reactivity of mesenteric arteries (MA). In the study of examining the effects of sugar supplementation, we demonstrated that only fructose intake causes hypertriglyceridemia and increases in body and liver weight in female rats. Our data also showed that the endothelium-dependent vasodilation (EDV) was impaired in MA of animals supplemented with fructose but not glucose. In the study of assessing the effect of diabetes, EDV was impaired in MA from both models of diabetes compared to controls, regardless of sex. In female ZDF, the relative importance of endothelium-derived hyperpolarizing factor (EDHF, a major EDRF) was reduced along with a decrease in SKca mRNA expression, while importance of NO as well as eNOS mRNA expressions were increased in MA of this experimental group. In MA of male ZDF, however, the role of NO was reduced. Furthermore, vascular smooth muscle sensitivity to NO was increased in ZDF rats, regardless of sex. In UCD-T2DM model, MA of female diabetic rats showed a greater impairment of EDV compared to that in pre-diabetic and male diabetic rats as well as a reduction in eNOS mRNA expression compared to their male counterparts. Diabetes also significantly increased sensitivity of MA to contractile agents in females compared to males and pre-diabetic females. Finally, the relative importance of EDHF to vascular regulation was lost in pre-diabetic and diabetic rats, regardless of sex. Accordingly, the mRNA expression of SKca was decreased in MA of both pre-diabetic and diabetic male and female rats. In conclusion, this study suggests that the type of sugar supplementation determines adverse metabolic and vascular changes in female rats. Furthermore, the 9 effects of type 2 diabetes on MA are sex- and rat model- specific. Finally, we showed a greater predisposition of MA to vascular injury in diabetic female UCD-T2DM rats.

Communities of granivorous desert rodents are structured by habitat selection and may be influenced by either predatory risk or resources. To examine these hypotheses, I manipulated illumination using lanterns, parachute canopies, or natural moonlight and resources using seeds. Foraging behavior is risk-sensitive; increased illumination reduces foraging in open areas while adding shadows to open areas using parachutes increases foraging there. Foraging behavior is also affected by resource enrichments. Differences among species in habitat selection were determined by specific abilities to detect and avoid predators. The least vulnerable species, Dipodomys deserti, foraged heavily in the open and was largely unaffected by treatments; other species of kangaroo rats and kangaroo mice also prefer the open, but responded to both risk and resource manipulations; highly vulnerable Peromyscus maniculatus was always restricted to bushes even under the most favorable circumstances; Perognathus longimembris was restricted to bushes in the absence of P. maniculatus in 1980 and was displaced from preferred microhabitats by the presence of kangaroo rats in 1981. A correlation between auditory bullar volume and use of open habitat by the various species in this community suggests that predatory risk provides an axis along which habitat segregation occurs. Predation can shape community structure by influencing foraging decisions of individuals. Desert rodents from North America and the Middle East have converged morphologically and perhaps in behavior and in community structure. Using desert rodent communities in the Great Basin Desert of U.S.A. and in the Negev Desert of Israel, I manipulated predatory risk in both communities and noted that foraging activity declines with increased predatory risk. Additional evidence suggests that predation also affects habitat selection behavior in both communities. Furthermore, differences in habitat utilization among species which promotes coexistence are related to morphological anti-predator specialization of the species. Predation appears to have shaped behavior and contributed to community structure in similar ways in both communities.

Thesis (PH.D. (Medical Sciences)) --University of Limpopo, 2010 / Refere to document

Thesis (Ph. D.)--Oregon State University, 2008. / Printout. Includes bibliographical references. Also available on the World Wide Web.

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Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2011. / ENGLISH ABSTRACT: The Rattus sensu lato complex, which harbours the important biomedical model species Rattus norvegicus, represents a group of rodents that are of clinical, agricultural and epidemiological importance. This study presents a comprehensive comparative molecular cytogenetic investigation of this complex. Karyotypes of 11 Rattus s. l. species and Hapalomys delacouri were analysed using conventional cytogenetic techniques. These data suggest that, contrary to previous claims, the usefulness of karyotypes for identifying these Asian murid species is limited, as few species-specific chromosomal characters could be identified. In order to understand the events that shaped the morphology and composition of the extant karyotypes, nine out of the 11 Rattus s. l. species were analysed by chromosome painting. This allowed the detection of a rare convergent sex-autosome translocation present in H. delacouri and B. savilei, whose establishment is hypothesised to have been favoured by the presence of interstitial heterochromatic blocks (IHBs) at the boundaries of the translocated segments. These results indicate that Rattus s. l. is characterised by slow to moderate rates of chromosome evolution in contrast to the extensive chromosome restructuring identified in most other murid rodents. Based on these data the first comprehensive putative Rattini ancestral karyotype was constructed. Their integration with published comparative maps enabled a revision of the previously postulated ancestral murid karyotype. BAC-mapping unequivocally demonstrated that the widely reported polymorphisms affecting chromosome pairs 1, 12 and 13 in the Rattus karyotypes are due to pericentric inversions. The analysis of genomic features, such as telomeres, Ag-NORs and satellite DNA suggest a constrained pattern of chromosome evolution. The investigated rat satellite I DNA family appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). The comparative nature of the study led to the further analysis of the species within Rattus s. l. complex and their possible involvement as reservoirs of scrub typhus using a qPCR gene expression approach based on real-time PCR. The structure and transcription of syndecan-4, which had previously been linked to Orientia tsutsugamushi (causative agent of scrub typhus) infection, was compared among Rattini (typhus-positive) and Murini (typhus-negative) rodents. Although, it was not possible to conclusively link the structural variation observed between Rattini and Murini with carrier status, a link was identified between underexpression of syndecan-4 in Murini and seropositive Rattini rodents, compared to those that were seronegative. This suggests that the reduced levels of syndecan-4 transcription in Murini and Rattini is linked to the poor carrier status of Murini, and to increased longevity of seropositive Rattini (i.e., predominant host of Orientia), highlighting aspects that need further investigation. / AFRIKAANSE OPSOMMING: Die Rattus sensu lato kompleks, wat die belangrike biomediese model spesie Rattus norvegicus huisves, bevat ‘n groep knaagdiere wat van kliniese, landbou, en epidiomologiese belang is. Hierdie studie bevat ‘n omvattende sitogenetiese molekulêre vergelyking binne hierdie kompleks. Die kariotipes van 11 Rattus s. l. spesies en Hapalomys delacouri is ondersoek met die gebruik van konvensionele sitogenetiese tegnieke. Die data dui daarop, in kontras met vorige bevindinge, dat die bruikbaarheid van kariotipes om Asiese knaagdiere te identifiseer beperk is, aangesien min spesies-spesifieke chromosoom merkers geidentifiseer kon word. Om die gebeure wat tot die morfologie en komposisie van die huidige kariotipes gelei het, te verstaan, is nege van die 11 Rattus s. l. spesies met behulp van chromosoom fluoressente hibridisasie ondersoek. Dit het die ontdekking van ‘n rare konvergente geslagschromosoom-outosoom translokasie in H. delacouri en B. savilei tot gevolg gehad. Die vaslegging hiervan is heel moontlik bevoordeel deur die teenwoordigheid van interkalerende heterchromatien blokke (IHBs) by die grens van die translokeerde segmente. Hierdie resultate dui daarop dat Rattus s. l. deur ‘n stadige tempo van chromosoom verandering gekenmerk word, wat in skrille kontras staan met die hoë aantal chromosoom herrangskikkings wat in meeste ander murid knaagdiere geidentifiseer is. Vanuit hierdie data kon die eerste oerouer kariotipe van die Rattini bepaal word. Die gebruik van hierdie data in kombinasie met beskikbare vergelykende kaarte het dit moontlik gemaak om die vorige hipotetiese oerouer murid kariotipe te hersien. BAC-kartering het dit moontlik gemaak om sonder twyfel vas te stel dat die polimorfisme wat chromosoom pare 1, 12 en 13 in die Rattus kariotipe affekteer, die resultaat van perisentriese omsetting is. Die analise van genomiese eienskappe, soos telomere, Ag-NORs en satelliet DNA dui op ‘n beperkte patroon van chromosoom evolusie. Die bestudeerde rot satelliet DNA familie blyk takson (Rattus) spesifiek te wees met ‘n onlangse oorsprong, wat ooreenstem met die terugvoer model van satellite-evolusie. Die vergelykende aard van hierdie studie het gelei tot die verdere analise van die spesies in die Rattus s. l. kompleks in terme van hul moontlike rol as draers van “scrub typhus” deur gebruik te maak van qPCR geen uitdrukking, wat gebasseer is op “real-time” PCR. Die struktuur en transkripsie van syndecan-4, wat in die verlede aan Orientia tsutsugamushi (veroorsakende agent van scrub typhus) infeksie gekoppel is, is tussen Rattini (typhuspositief) en Murini (typhus-negatief) knaagdiere vergelyk. Ten spyte daarvan dat dit nie moontlik was om die strukturele variasie tussen Rattini en Murini met draer status te koppel nie, is daar wel ‘n skakel tussen die verlaagde uitdrukking van syndecan-4 in Murini en seropositiewe Rattini knaagdiere, in vergelyking met die wat sero-negatief was, gevind. Dit stel voor dat die verlaagde vlakke van syndecan-4 transkripsie in Murini en Rattini aan die swak draer status van Murini, asook die verhoogde langslewendheid van sero-positiewe Rattini (i.e., oorheersende gasheer van Orientia), gekoppel is. Hierdie bevindinge beklemtoon sekere belangrike aspekte vir verdere navorsing.

The pattern of geographic variation in tree-climbing ability of Peromyscus maniculatus was used as a natural experiment to examine the interaction of natural selection, genetic drift, and gene flow. The divergence in climbing behavior among lab-reared mice derived from adults trapped in forest, woodland, and desert habitats was compared with a series of adaptive and non-adaptive hypotheses of evolutionary change. Natural selection was predicted to produce better climbers in forests and woodlands than in deserts whereas divergence due to genetic drift was expected to be independent of habitat type. Gene flow between neighboring habitats was predicted to reduce differentiation in climbing traits. Tree-climbing ability was measured by determining the maximum diameter artificial trunk (rod) that a mouse could climb in escaping from a lighted, confined area. Larger diameter rod scores reflect better climbing abilities (Horner 1954). Comparisons of mean rod climbing scores between subspecies and among forest, woodland, and desert habitats reveal that P. m. rufinus, sampled from forest and woodland, is a better climber than P. m. sonoriensis, sampled from woodland and desert habitats. This is consistent with the hypothesis that natural selection has produced subspecies level adaptation in climbing behavior. However, the climbing ability of P. m. sonoriensis sampled from woodland habitats on isolated mountaintops, although slightly divergent from populations in adjacent desert scrub habitats, has not evolved in response to natural selection to the degree expected from the observed subspecies level adaptation. Additionally, populations of unknown subspecific status sampled from desert grassland habitat, adjacent to woodland P. m. rufinus, have climbing abilities that are not significantly different from woodland forms. Thus, evolution in certain populations is constrained. If gene flow from desert populations into woodland mountaintop populations is constraining evolution, then mountaintop populations should have high trait variances. Analysis of the within population variance does not support this hypothesis. Other lines of evidence that indicate gene flow is low or moderate are reviewed. In conclusion, adaptation to local habitats is constrained, perhaps by restrictive genetic correlations and/or lack of sufficient time to respond to natural selection for climbing ability. As a result, long periods of consistent selection are necessary to produce the pattern of subspecific adaptation in climbing behavior. (Abstract shortened with permission of author.)