Life Sciences Commons^™

A New Fossil Wood Species Of Ziziphus From The Middle Miocene Of Türkiye And Its Palaeoenvironmental Evaluation, Ünal Akkemi̇k, Özlem Toprak

Turkish Journal of Botany

The purpose of this study is to describe a new fossil wood from the Middle Miocene of South Anatolia (Mersin) and to identify it and evaluate its palaeoenvironmental implications. Thin sections of transverse, tangential, and radial surfaces were examined and described using the terminology of the International Association of Wood Anatomists. The wood was determined to have characteristics of Ziziphus (Rhamnaceae). It is the first fossil wood of Ziziphus and is described as Ziziphoxylon sayaz Akkemik sp. nov. It is from the Middle Miocene Climate Optimum (MMCO), which is a relatively warm interval in the Miocene. Indistinct annual growth ring …

Momkk1 And Moatg1 Dichotomously Regulating Autophagy And Pathogenicity Through Moatg9 Phosphorylation In Magnaporthe Oryzae, Yun Kong, Pusheng Guo, Jiayun Xu, Jiaxu Li, Miao Wu, Ziqi Zhang, Yifan Wang, Xinyu Liu, Leiyun Yang, Muxing Liu, Haifeng Zhang, Ping Wang, Zhengguang Zhang

School of Medicine Faculty Publications

Autophagy is a central biodegradation pathway critical in eliminating intracellular cargo to maintain cellular homeostasis and improve stress resistance. At the same time, the key component of the mitogen-activated protein kinase cascade regulating cell wall integrity signaling MoMkk1 has an essential role in the autophagy of the rice blast fungus Magnaporthe oryzae. Still, the mechanism of how MoMkk1 regulates autophagy is unclear. Interestingly, we found that MoMkk1 regulates the autophagy protein MoAtg9 through phosphorylation. MoAtg9 is a transmembrane protein subjected to phosphorylation by autophagy-related protein kinase MoAtg1. Here, we provide evidence demonstrating that MoMkk1-dependent MoAtg9 phosphorylation is required for phospholipid …

Two Dot1 Enzymes Cooperatively Mediate Efficient Ubiquitin-Independent Histone H3 Lysine 76 Tri-Methylation In Kinetoplastids, Victoria Frisbie, Hideharu Hashimoto, Yixuan Xie, Francisca De Luna Vitorino, Josue Baeza, Tam Nguyen, Zhangerjiao Yuan, Janna Kiselar, Benjamin Garcia, Erik Debler

Department of Biochemistry and Molecular Biology Faculty Papers

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx₆K) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site …

A New Permineralized Corypha-Type Coryphoid Palm Stem From K-Pg Of India: Anatomy, Systematics, Saprophytic Fungi, And Paleoecology, Ashif Ali, Kaustav Roy, Biswajit Mukherjee, Subir Bera, Mahasin Khan

Turkish Journal of Botany

Palms are known to be an important and diverse angiosperm component in the Deccan Intertrappean beds of Central India. However, the report of fossilized palm stems inhibiting saprophytic fungal remains is empty in the field of paleobotany. Here, we document for the first time the occurrence of fungal remains in a petrified palm stem collected from the latest Maastrichtian (Late Cretaceous)-earliest Danian (early Paleocene) sediments of the Deccan Intertrappean beds of Madhya Pradesh, Central India. The anatomical features of the fossil stem are characterized by the presence of Corypha-type general stem pattern (progressive decrease of fibrous parts of fibrovascular bundles, …

Dorycnium Vuralii (Fabaceae), A New Species From Türkiye, Bilal Şahi̇n, Seher Karaman, Mevlüde Alev Ateş, Zeki Aytaç

Turkish Journal of Botany

The present study describes a new species Dorycnium vuralii (Fabaceae) from Çankırı, Türkiye. The new species is compared morphologically to the taxa of sect. Bonjeanea and sect. Dorycnium along with pollen micromorphology, leaflet, and seed micromorphology. The geographical distribution of Dorycnium vuralii is mapped. The phylogenetic relationships between the new species and other closely related species in the genus are inferred based on DNA data from both cpDNA and nrDNA (rbcL1&ITS). Although phylogenetic implications are different in the two DNA barcoding regions, D. vuralii is shown to be a new species in both molecular data. The new species is assessed …

Floodplain Restoration And Its Effects On Summer Water Temperature And Macroinvertebrates In Whychus Creek, Oregon (Usa), Wesley N. Noone, Patrick M. Edwards, Yangdong Pan, Colin R. Thorne

Environmental Science and Management Faculty Publications and Presentations

Stream restoration is a proposed climate adaptation tool; however, outcomes of floodplain restoration on stream temperature have been debated. Despite a growing number of studies that investigated water temperature in restored streams, few have quantified temperature variations in new habitat types created by restored hydrogeomorphic processes to explore the effects on aquatic macroinvertebrates. We evaluated the hypotheses: (1) restoration increases habitat diversity, (2) habitat diversity increases water temperature variability, and (3) restoration increases the diversity of macroinvertebrate assemblage and temperature associations. In August 2021, we collected environmental data to describe the aquatic habitats, water temperature and quality (continuous and discrete), …

Visual Outcome And Ocular Complications In Patients With Lacrimal Gland Carcinoma After Eye-Sparing Surgery And Adjuvant Radiation Therapy, Zhenyang Zhao, Steven Jay Frank, Jing Ning, Jiawei Zhao, Xinyang Jiang, Amy C Schefler, Amy Moreno, Brandon Gunn, Renata Ferrarotto, Bita Esmaeli

Faculty, Staff and Student Publications

Background: We report visual outcomes and ocular complications in patients with lacrimal gland carcinoma who had eye-sparing surgery followed by radiotherapy.

Methods: This review included consecutive patients with lacrimal gland carcinoma who underwent eye-sparing surgery and adjuvant radiotherapy or concurrent chemoradiation therapy between 2007 and 2018. Clinical data, including details of ophthalmological examinations and radiation treatment were reviewed.

Results: The study included 23 patients, 15 males and 8 females, with median age 51 years. Twenty patients (87%) received intensity-modulated proton therapy; 3 (13%) received intensity-modulated radiotherapy. Nineteen patients (83%) received concurrent chemotherapy. After a median follow-up time of 37 months …

Durvalumab And Tremelimumab Before Surgery In Patients With Hormone Receptor Positive, Her2-Negative Stage Ii-Iii Breast Cancer, Haven R Garber, Sreyashi Basu, Sonali Jindal, Zhong He, Khoi Chu, Clinton Yam, Beatriz E Adrada, Padmanee Sharma, Elizabeth A Mittendorf, Jennifer K Litton

Faculty, Staff and Student Publications

A clinical trial was conducted to assess the feasibility of enrolling patients with Stage II or III hormone receptor positive (HR+)/HER2-negative breast cancer to pre-operative dual PD-L1/CTLA-4 checkpoint inhibition administered prior to neoadjuvant chemotherapy (NACT). Eight eligible patients were treated with upfront durvalumab and tremelimumab for two cycles. Patients then received NACT prior to breast surgery. Seven patients had baseline and interval breast ultrasounds after combination immunotherapy and the responses were mixed: 3/7 patients experienced a ≥30% decrease in tumor volume, 3/7 a ≥30% increase, and 1 patient had stable disease. At the time of breast surgery, 1/8 patients had …

Single-Cell Analysis Of Age-Related Changes In Leukocytes Of Diabetic Mouse Hindpaws, James M Nichols, Hoang Vu Pham, Eric F Lee, Rajasekaran Mahalingam, Andrew J Shepherd

Faculty, Staff and Student Publications

Complications associated with Type 1 and Type 2 diabetes, such as diabetic peripheral neuropathy and diabetic foot ulcers, are a growing health-care concern. In addition, this concern increases as diabetic patients age due to their increased susceptibility to complications. To address this growing problem, it is important to understand fluctuations in physiology which lead to pathological changes associated with the metabolic disturbances of diabetes. Our study explores dysregulation of immune cell populations in the hindpaws of healthy and diabetic mice at 12 and 21 weeks of age using single-cell RNA sequencing to provide insight into immune disruptions occurring in the …

Synthetic Pet From Ct Improves Diagnosis And Prognosis For Lung Cancer: Proof Of Concept, Morteza Salehjahromi, Tatiana V Karpinets, Sheeba J Sujit, Mohamed Qayati, Pingjun Chen, Maliazurina B Saad, Lingzhi Hong, Ajay Sheshadri, Julie Lin, Mara B Antonoff, Boris Sepesi, Edwin J Ostrin, Iakovos Toumazis, Peng Huang, Chao Cheng, Tina Cascone, Natalie I Vokes, Carmen Behrens, Jeffrey H Siewerdsen, John D Hazle, Joe Y Chang, Jianhua Zhang, Yang Lu, Myrna C B Godoy, Caroline Chung, David Jaffray, Ignacio Wistuba, J Jack Lee, Ara A Vaporciyan, Don L Gibbons, Gregory Gladish, John V Heymach, Carol C Wu, Jianjun Zhang, Jia Wu

Faculty, Staff and Student Publications

[18F]Fluorodeoxyglucose positron emission tomography (FDG-PET) and computed tomography (CT) are indispensable components in modern medicine. Although PET can provide additional diagnostic value, it is costly and not universally accessible, particularly in low-income countries. To bridge this gap, we have developed a conditional generative adversarial network pipeline that can produce FDG-PET from diagnostic CT scans based on multi-center multi-modal lung cancer datasets (n = 1,478). Synthetic PET images are validated across imaging, biological, and clinical aspects. Radiologists confirm comparable imaging quality and tumor contrast between synthetic and actual PET scans. Radiogenomics analysis further proves that the dysregulated cancer hallmark pathways of …

Polyamine-Mediated Ferroptosis Amplification Acts As A Targetable Vulnerability In Cancer, Guoshu Bi, Jiaqi Liang, Yunyi Bian, Guangyao Shan, Yiwei Huang, Huan Zhang, Zhencong Chen, Mengnan Zhao, Hong Fan, Qun Wang, Boyi Gan, Cheng Zhan

Faculty, Staff and Student Publications

Targeting ferroptosis, an iron-dependent form of regulated cell death triggered by the lethal overload of lipid peroxides, in cancer therapy is impeded by our limited understanding of the intersection of tumour’s metabolic feature and ferroptosis vulnerability. In the present study, arginine is identified as a ferroptotic promoter using a metabolites library. This effect is mainly achieved through arginine’s conversion to polyamines, which exerts their potent ferroptosis-promoting property in an H2O2-dependent manner. Notably, the expression of ornithine decarboxylase 1 (ODC1), the critical enzyme catalysing polyamine synthesis, is significantly activated by the ferroptosis signal——iron overload——through WNT/MYC signalling, as well as the subsequent …

Three-Dimensional Optothermal Manipulation Of Light-Absorbing Particles In Phase-Change Gel Media, Pavana Siddhartha Kollipara, Zilong Wu, Kan Yao, Dongdong Lin, Zhengyu Ju, Taizhi Jiang, Jie Fang, Jingang Li, Brian A Korgel, Joan M Redwing, Guihua Yu, Yuebing Zheng

Faculty, Staff and Student Publications

Rational manipulation and assembly of discrete colloidal particles into architected superstructures have enabled several applications in materials science and nanotechnology. Optical manipulation techniques, typically operated in fluid media, facilitate the precise arrangement of colloidal particles into superstructures by using focused laser beams. However, as the optical energy is turned off, the inherent Brownian motion of the particles in fluid media impedes the retention and reconfiguration of such superstructures. Overcoming this fundamental limitation, we present on-demand, three-dimensional (3D) optical manipulation of colloidal particles in a phase-change solid medium made of surfactant bilayers. Unlike liquid crystal media, the lack of fluid flow …

Scale Of Patchiness Affects The Relation Between Forage Quality And Patch Choice By Cattle, Wallis Devries, M F. Laca, E A. Laca

IGC Proceedings (1977-2023)

We predicted and tested the effects of scale of heterogeneity on movements and selectivity of a large grazer in a controlled field experiment. We created random mosaics of short/high quality and tall/low quality grass patches in equal proportion at grid sizes of 2x2 m and 5x5 m. Subsequently, we monitored the foraging behavior of four steers in 16 20x40 m plots over 30-minute periods. As predicted, the animals selected the short patches both by walking in a nonrandom manner and by concentrating their grazing time. Selectivity was more pronounced in large patches than in small ones. In contrast, the number …

Spatial Analysis Of Land Use By Cattle Herds In A Village Of The Sudanese Zone In Senegal. Application For Grazing System Improvement, A Ickowicz, J C. Usengumuremyi, D Bastien, N De Choudens

IGC Proceedings (1977-2023)

Spatial analysis of land use by cattle herds in the sub-humid area of Senegal is conducted through the utilisation of a Geographic Information System. This tool allows us to establish relationships between spatial practices, ruminant nutrition and performances. It gives leads to proposals for the improvement of the extensive ruminant feeding system.

Using Cuticular Wax Alkanes And Computer Simulation To Estimate Diet Selection, Herbage Intake And Nutrient Cycling In Grazing Sheep, H Dove, R J. Simpson

IGC Proceedings (1977-2023)

In grazing ewes, plant cuticular wax alkanes were used as markers to estimate diet selection, herbage intake, N intake and N excretion in faeces. Pasture and animal data were then used as inputs to the decision-support system GrazFeed, which simulates grazing and digestion to predict herbage intake, N intake and N excretion. Estimated and predicted intakes agreed closely, especially for N intake, and it is concluded that, subject to further investigation of the possibility that GrazFeed slightly under-estimated faecal N excretion, the close agreement between estimated and predicted OM and N intakes suggests that this combined use of alkane methods …

Effect Of Species Horizontal Distribution On Defoliation Of Ryegrass-Clover Swards Grazed By Sheep, P C. De Faccio Carvalho, F Louault, M Lafarge

IGC Proceedings (1977-2023)

Defoliation events on labelled white clover (Trifolium repens) growing points or ryegrass (Lolium perenne) tillers were measured during grazing tests by sheep with swards consisting of mixed ryegrass-clover (MIX) or alternate strips of clover and ryegrass (STRIP). Sward surface height was maintained at 6.4 cm by lawnmower cuts in order to obtain a similar surface height for both species. On average, during 13 grazing tests in STRIP and 11 in MIX swards, clover was the more defoliated species : 23.3% of the growing points in STRIP and 26.5% in MIX swards were defoliated compared to 16.2% …

Foraging Behavior Of Zebu Cattle Grazing Deciduous Forest, L Ortega, J Castillo, F Rivas

IGC Proceedings (1977-2023)

The objective of this study was to determine whether the foraging behavior of Zebu cattle in deciduous forest was affected by time of the year. Data were recorded during the wet, nortes and dry seasons. Ten Zebu cows were used to record biting rate. Intake and bite size was estimated using three esophageally fistulated animals. Cattle browsed shrubs and trees in the wet season and ingested litter leaves in the dry season which resulted in differences of ingestive behavior. In general, bite size and intake were higher in the wet season and decreased during the nortes and dry seasons.

Behaviour Of Cattle On Two Different Types Of Upland Pastures, D Macesic, M Knezevic

IGC Proceedings (1977-2023)

The purpose of this research was to study the influence of the quality of pastures on the behaviour of cows in a 'cow-calf' system. The behaviour was measured by the four principal activities of the herd: grazing, lying, 'roaming' and insect repelling, and it is presented with relative indicators. The trial was conducted on pasture areas of the Faculty of Agriculture, University of Zagreb, at the altitude of 650- 850 m. The influence of the pasture quality on the behaviour of cattle on pasture was studied on two different types of pastures: a natural unreclaimed pasture belonging to the Arrhenatheretum …

Foraging Behaviour Of Heifers, Sheep And Goats In Grass-Legume Cafeteria, J P. Singh, Vinod Shankar, V S. Upadhyay

IGC Proceedings (1977-2023)

The paper reports findings of a grazing trial with heifers, sheep and goats in a grass–legume cafeteria involving 45x10 m alternate strips of 18 grasses and 18 legumes. In the first year heifers were grazed. Sheep were introduced in the second year and goats in the third year. The stocking rate was 1.5 ACU/ha. Foraging behaviour of three kinds of animals differed in many respects with grazing and rest durations, choice of species in the forenoon and afternoon and in different seasons. Heifers, by and large, preferred grasses over legumes and browse. Sheep, on the contrary, preferred legumes over grasses …

Effects Of Defoliation Frequency On Foraging Selective Behaviour In Pasture With Paspalum Dilatatum, G L. Acosta, A T. Ayala Torales, V A. Deregibus

IGC Proceedings (1977-2023)

The objective was to assess defoliation effects exerted by sheep grazing on a pasture composed by falaris and dallisgrass, at two phenological stages during spring and summer. A sown pasture of Phalaris aquatica and Paspalum dilatatum were grazed at two phenological stages: stage I (SI), with no more than 5% of reproductive tillers, and stage II (SII), with at least 70% of reproductive tillers. Tillers of both grass species were marked with plastic colour rings along two transects in each plot. Phenological stage of tillers, and the number, age and length of each leaf per tiller were registered. Tiller defoliation …

Characterization Of Grazing Patterns In Cool-Season Annual And Warm-Season Perennial Grass Pastures, G E. Aiken, M S. West, D I. Bransby

IGC Proceedings (1977-2023)

Pastures are often either under- or over-grazed, which can affect both pasture sustainability and livestock performance. Disk meter heights were measured for rye (Secale cereale L.) -ryegrass (Lolium L. multiflorum Lam.) pasture to characterize stocking rate (2.5, 3.7, and 4.9 steers/ha) effects on grazing patterns. In another study, grazing indices were calculated for bermudagrass [Cynodon dactylon (L.) Pers.] to describe pasture utilization over time for three stocking rates (3.0, 5.9, 8.9 steers/ha). Distributions of DMH for rye-ryegrass showed distinct grazing patterns for each stocking rate, with the distributions changing from bimodal to multi-modal from heavy to light …

Border Effects On Cattle Grazing Preference, G E. Shewmaker, H F. Mayland, S B. Hansen

IGC Proceedings (1977-2023)

The objective was to examine the effect of row position on cattle grazing preference. Grazing preference of eight tall fescues [Festuca arundinacea (Schreb.)] was evaluated by ocular preference scores at 30 hr (PS30) and 48 hr (PS48). Six rows of a cultivar—numbered consecutively within each plot from left to right—formed one plot. Rows 1&6 were on the outside edges of the plot and rows 3&4 were in the middle. Within a replication, rows 1 and 6 were adjacent to rows 6 and 1 of adjacent plots, respectively. During the first year, row position was not a significant effect. However, …

Intake And Diet Selection By Sheep Grazing Grass/Clover Patches, I J. Gordon, A W. Illius

IGC Proceedings (1977-2023)

The effects of the spatial dispersion of ryegrass (Lolium perenne L) and clover (Trifolium repens L), at the feeding station scale, on diet composition and feeding behaviour were studied for sheep. There were no significant changes in diet composition with changes in the spatial dispersion of sward components. Bite size, bite rate and intake rate did increase as the species became more aggregated.

Relationships Between The Nutrient Content Of Irrigated Pasture On Offer And That Selected By Grazing Dairy Cows, W J. Wales, C R. Stockdale, P T. Doyle

IGC Proceedings (1977-2023)

An experiment was conducted to determine the dry matter, energy, crude protein and fibre intake by dairy cows in late lactation when grazing perennial pasture offered at allocations of 15, 20, 30 and 40 kg DM/cow.day. The cows consistently selected a diet 10% higher in digestibility than that on offer. In contrast, cows selected diets with crude protein levels increasing from 22% to 40%, above that in pasture on offer, as pasture allocation increased. A similar pattern was observed for the intake of white clover (Trifolium repens L). The increase in the concentration of crude protein in the diet …

Species Preference Influences On Cattle Grazing Behaviour, G P. Cosgrove, C B. Anderson, R H. Fletcher

IGC Proceedings (1977-2023)

Lotus corniculatus offers specific nutritional benefits to animals, but exploiting these advantages in grazing systems depends on the proportion of lotus in the feed offered and the animals' preference, hence desire to select for it. To determine preference for lotus, heifers were offered free-choice in contrasting, spatially separated but adjacent monocultures of ryegrass-lotus or red clover-lotus. Following a one-week period to adjust to the species offered and their arrangement, 10 young heifers were observed at 10-minute intervals during daylight hours, and the species they were on and whether or not they were grazing was recorded. This procedure was conducted in …

Partial Preference Of Grazing Cattle For Contrasting Legume Swards, C.H. E.C. Poli, J Hodgson, G P. Cosgrove, G C. Arnold

IGC Proceedings (1977-2023)

Yearling heifers in groups of 3 grazed 405 m2 plots made up of alternating 2.4m wide strips of white clover/birdsfoot trefoil (WC+BT) or red clover (RC) in the proportions of 80:20, 67:33, 33:67 and 20:80 for periods of 3 days over four replicates in time, balanced for effects of previous treatment. Observation of the distribution of grazing activity and biting rate were made over 3 hour periods each evening. Biting rates were consistently higher on (WC+BT) than RC (52.3 vs 46.3 ± 0.59 bites.min-1 P(0.0001). Animals initially showed partial preference for the minor sward component in each treatment but regression …

The Use Of Vibration Analysis And Telemetry To Measure Bite Frequency And Intensity In Free-Ranging Horned Ruminants, P R. Lawrence, K Becker

IGC Proceedings (1977-2023)

An apparatus is described which detects and measures the vibrations in a ruminant’s horn especially those produced by the animal’s teeth. Vibrations are transmitted by radio to a portable computer where those produced as a result of eating and ruminating can be characterised by their intensity, length and frequency.

Influence Of Vegetation Patch Characteristics On Discriminatory Grazing By Dairy Cows, W M. Griffiths, J Hodgson, G C. Arnold, C W. Homes

IGC Proceedings (1977-2023)

Two studies involving the sequential grazing of sets of patches on a perennial ryegrass (Lolium perenne) sward were carried out to investigate the effects of patch characteristics on the selective behaviour of grazing cattle. Experiment 1 involved a range of combinations of sward height (8.9 - 19.6 cm) and bulk density (1.33 - 1.67 mg DM/cm3). Distribution of grazing activity (number of bites or residence time) was strongly and positively related to patch height, but additional effects of variation in bulk density were limited. In Experiment 2 patches were manipulated to offer contrasts in both height (13.4 and …

Shade For Cattle On Pasture: A Guide For Ontario Producers, E J. Finegan, T M. Widowski

IGC Proceedings (1977-2023)

In tropical climates, adequate shade may be essential to ensure the survival and productivity of grazing animals, but in the temperate Ontario climate, the necessity or benefits of providing shade for grazing cattle are less clear, and have proved controversial. Meteorological data indicate that beef cattle in Ontario may be at risk of suffering from heat stress on more than 25% of days during July and August, and may decrease feed intake and benefit from the provision of shade for more than 50% of days during the two hottest summer months. A booklet, entitled ‘Beat the Heat. A Guide …

Remodeling Anaplastic Thyroid Cancer's Aggressive Profile And Metabolic Signature By Natural Alkaloid Berberine, Tara Elizabeth Jarboe

NYMC Student Theses and Dissertations

Anaplastic thyroid cancer is a rare, fatal cancer with a five-year survival of 4%. Universally diagnosed at stage IV, anaplastic thyroid cancer is characterized by its lack of differentiation, rapid proliferative rate, highly inflammatory tumor microenvironment, and metabolic dysregulation. Refractory to all established therapies, anaplastic thyroid cancer requires a novel therapeutic approach that targets all of these drivers of anaplastic thyroid cancer carcinogenesis. We propose natural alkaloid berberine as a therapeutic with multitarget efficacy to alter mitochondrial metabolism and reprogram anaplastic thyroid cancer’s aggressive phenotype. Our in vitro model uses monocyte cell line U937, anaplastic thyroid cancer cell lines T238 …