Biology Commons^™

Riparian Plant Isotopes Reflect Anthropogenic Nitrogen Perturbations: Robust Patterns Across Land Use Gradients, Steven J. Hall, Rebecca L. Hale, Michelle A. Baker, David R. Bowling, James R. Ehleringer

Biology Faculty Publications

Riparian plants incorporate nitrogen (N) from aquatic, terrestrial, and atmospheric sources, and their stable isotope compositions (δ¹⁵ N) may reflect land use impacts on N sources and transformations over scales of sites to watersheds. We surveyed leaf δ¹⁵ N values of 11 common riparian tree, shrub, and herbaceous species from 20 streams and rivers spanning three fifth-order watersheds in northern Utah, USA (n - 255 sites and 819 leaf samples). Streams spanned undeveloped montane forests to suburban, urban, and agricultural lands. Mean species-specific differences in leaf δ¹⁵N values were relatively small within sites (1.2 ± 2.2‰), …

Short Report: Description And Distribution Of Wagtails "Family Motacillidae" With Reference To Pakistan, Nadia Yousuf, Kainaat William, Madeeha Manzoor, Balqees Khanum

Journal of Bioresource Management

In the current study, Wagtails of the Family Motacillidae were studied in Pakistan. Thirteen species and sub-species were found in different regions. Their characteristics were observed, photographs were taken, previous distributions of these species were analyzed, and a new distribution of each species was reported in this study. During study, the scavenging role of these birds was identified, and it was hoped that wagtails may play an important role in the absence of the vultures after recent downfalls in major scavengers. However, these important effects were not observed in the wagtails, and probably will not occur until their populations increase …

In Vitro Culturing And Harvesting Of Human Plucked Hair Follicles, Iram Rehman, Attika Rehman, Samina Jalali

Journal of Bioresource Management

Human hair follicles are miniature hair growing organs. A common human hair disorder is androgenetic alopecia (AGA), which becomes a medical problem only when the hair loss is subjectively seen as excessive, premature, and distressing on the scalp. The objectives of the present study were to culture the hair stem cells in vitro and to study the morphology of the cultured cells for the treatment of AGA. The present study proposes that plucked human hairs are a cheap source to treat male baldness and in vitro culturing of hair follicle cells is the potential method to apply the cultured cells …

Distribution And Habitat Analysis For Freshwater Turtles Of River Indus And Some Of Its Tributaries In Khyber Pakhtunkhwa And Punjab, Pakistan, Malik Ghulam Sarwar, Fakhar -I- Abbas, Inayat Ali Shahjehan

Journal of Bioresource Management

This study was conducted to investigate the relative abundance and habitat analysis of freshwater turtles of Pakistan. Eighty two individuals of seven species of turtles at sixteen different sites in River Indus and some of its tributaries in Khyber Pakhtunkhwa (KP) and Punjab were recorded; these include both soft and hard shell freshwater turtles. The species documented were, Kachuga smithii, Kachuga tecta, Geoclemys hamiltonii, Aspideretes gangeticus, Aspideretes hurrum, Chitra indica and Lissemys punctata. The L. punctata was the most common, with relative frequency (RF) of 24.4%, followed by A. gangeticus (18.3%), A. hurum (17.1%), C. indica (17.1%), K. smithii (12.2%), …

A Study Of Dna Protective Ability Of Peels Of Different Citrus Species, Nehrish Nisar, Kainaat William, Azra Khanum

Journal of Bioresource Management

The aim of the present study was to assess the DNA protection ability, free radicals scavenging activity, and phytochemical constituents of peel extracts of various species of citrus. Results showed the presence of carbohydrates, amino acids, glycosides, tannins, steroids and alkaloids. DNA protection assay showed maximum protection with methanolic extracts of peels of C. limon, C. reticulata, C. aurantium and C. sinensis as compared to C. limetta which showed less protection. DPPH assay used to assess the antioxidants showed the highest activity in the methanolic extract of peels of C. reticulata and C. aurantium with 75% and 86% respectively at …

The Distribution, Population Status, And Wildlife Product Trade Of Himalayan Musk Deer In Gilgit-Baltistan, Pakistan, Fakhar -I- Abbas, Thomas P. Rooney, Afsar Mian, Zahid Iqbal Bhatti, Jibran Haider

Journal of Bioresource Management

Himalayan musk deer (Moschus chrysogaste leucogaster) is an IUCN Red List Endangered species that reaches its western range limit in Pakistan, although its distribution or population size is unknown. Here, we mapped its distribution, described habitat preferences, estimated population sizes, recruitment and mortality, and reported the market values of musk deer wildlife products. We used two approaches: analyzing local wisdom (traditional ecological knowledge) through the use of questionnaires, and conducting confirmatory field surveys of selected areas. Questionnaire respondents indicated musk deer sightings in 28 of 84 localities; mainly in Himalayan dry temperate forests with >20% forest cover. There …

Naphthalene Acetic Acid And Benzylaminopurine Enhance Growth And Improve Quality Of Organic Spinach In Kitchen Gardens, Duad Ahmed Awan, Faheem Ahmad, Sharmin Ashraf

Journal of Bioresource Management

The present study was conducted at the Kitchen Gardening Training Centre, Faisalabad, Pakistan to evaluate the effect of the plant growth regulators Naphthalene Acetic Acid (NAA) and Benzylaminopurine (BAP), on the growth and yield of organic spinach (Spinacia oleracea L.) in kitchen gardening. Different combinations and concentrations of NAA and BAP were tested to evaluate different vegetative parameters. The data were recorded at 40 and 60 days after sowing (DAS). Maximum plant height at 40 DAS was recorded for the combined effect of NAA and BAP at a concentration of 1000 μM (each), while BAP alone at 100 μM concentration …

Susceptibility Of Nppa And Il6 With Type 2 Diabetes And Hypertension In Punjab, Pakistan, Andleeb Batool, Riffat Iqbal, Maryam Mukhtar, Hong Xue

Journal of Bioresource Management

Type 2 Diabetes (T2D) and Hypertension are the major health issues affecting quality of life of young ages throughout the world, especially the third world countries facing more complications with diabetes due to poor disease management. The present study was conducted to explore the association of genetic polymorphism with T2D and hypertension in the Punjabi population. The case control study was conducted comprising of 288 patients (118 male, 170 female) and 170 controls (104 male, 66 female). The selected genes along SNPs were NPPA (rs5064 G>A, rs5063 C>T) and IL6 (rs1800796 C>G). DNA was amplified by Nested …

Species Diversity, Distribution And Seasonal Abundance In Mangrove Associated Molluscs Along The Karachi Coast, Pakistan, Zia Ullah, Itrat Zehra, Muhammad Asif Gondal

Journal of Bioresource Management

Mangrove or Mangal vegetation are typical wetland ecosystems found in coastal deposits of mud and silt throughout the tropics and some distance into the sub-tropical latitude. Species diversity, distribution, seasonal abundance in population and behavioral responses of mangrove associated molluscs (gastropods and bivalves) were investigated in two mangal areas: Sandspit and Korangi, along the Karachi coast of Pakistan. For sampling, a fixed route was followed throughout the study period and the samples were collected and observations were made from HTZ to LTZ. Fourteen species of molluscs (5 Prosobranchia; 6 Pulmonata; 1 Opisthobranchia and 2 Lamellibranchia) belonging to ten families were …

Performance Of Exotic Tulip Cultivars Under Agro-Climatic Conditions Of Peshawar, Muhammad Ali, Abdul Mateen Khattak, Kalim Ullah, Muhammad Ibrahim

Journal of Bioresource Management

The performance of ten exotic tulip cultivars under agro-climatic conditions of Peshawar was studied at Ornamental Nursery, Department of Horticulture, The University of Agriculture Peshawar, Pakistan during the year 2013-14. The experiment was laid out in Randomized Complete Block (RCB) Design with three replications. Ten cultivars of tulips viz., Bastogne, Don Quichotte, China Town, White Dream, Red Riding Hood, Mascotte, Orange Angelique, Strong Gold, Rajka and Romantic Sunset were tested for their performance. Significant differences (P≤0.05) were observed among the cultivars regarding various parameters. The cultivar “Don Quichotte” produced the maximum number of leaves per plant (8.1), bulbs per plant …

Mechanosensitive Channel Msl8 Regulates Osmotic Forces During Pollen Hydration And Germination, Eric S. Hamilton, Gregory S. Jensen, Grigory Maksaev, Andrew Katims, Ashley M. Sherp, Elizabeth S. Haswell

Biology Faculty Research

Pollen grains undergo dramatic changes in cellular water potential as they deliver the male germ line to female gametes, and it has been proposed that mechanosensitive ion channels may sense the resulting mechanical stress. Here, we identify and characterize MscS-like 8 (MSL8), a pollen-specific, membrane tension–gated ion channel required for pollen to survive the hypoosmotic shock of rehydration and for full male fertility. MSL8 negatively regulates pollen germination but is required for cellular integrity during germination and tube growth. MSL8 thus senses and responds to changes in membrane tension associated with pollen hydration and germination. These data further suggest that …

The Potential For A Blood Test For Scabies, Larry G. Arlian, Hermann Feldmeier, Majorie S. Morgan

Biological Sciences Faculty Publications

Scabies, caused by the mite S. scabiei that burrows in the skin of humans, is a contagious skin disease that affects millions of people worldwide. It is a significant public health burden in economically disadvantaged populations, and outbreaks are common in nursing homes, daycare facilities, schools and workplaces in developed countries. It causes significant morbidity, and in chronic cases, associated bacterial infections can lead to renal and cardiac diseases. Scabies is very difficult to diagnose by the usual skin scrape test, and a presumptive diagnosis is often made based on clinical signs such as rash and itch that can …

Super Staph In The Community: Is It Evolving?, Alan L. Gillen, Rachel Walters

Faculty Publications and Presentations

Staphylococcus aureus infections are a common cause of disease, particularly in colonized people. They frequently cause staph infections and are often dubbed “Super Staph” because they are virulent and multidrug resistant. Recently, a series of published articles have reported that community-acquired methicillin-resistant S. aureus (CA-MRSA) strains are evolving and becoming more prevalent in households. In contrast, health care acquired MRSA (HA-MRSA) is declining in the United States. The changing “Superbugs” have often been used as an example of “evolution in action.” Although MRSA infections have become more prevalent in the community, studies of college students carrying S. aureus and MRSA …

Migration In The Social Stage Of Dictyostelium Discoideum Amoebae Impacts Competition, Chandra N. Jack, Neil J. Buttery, Boahemaa Adu-Oppong, Michael Powers, Christopher R.L. Thompson, David Queller, Joan E. Strassmann

Biology Faculty Research

Interaction conditions can change the balance of cooperation and conflict in multicellular groups. After aggregating together, cells of the social amoeba Dictyostelium discoideum may migrate as a group (known as a slug) to a new location. We consider this migration stage as an arena for social competition and conflict because the cells in the slug may not be from a genetically homogeneous population. In this study, we examined the interplay of two seemingly diametric actions, the solitary action of kin recognition and the collective action of slug migration in D. discoideum, to more fully understand the effects of social competition …

Complete Mitochondrial Genome Of The Speckled Dace Rhinichthys Osculus, A Widely Distributed Cyprinid Minnow Of Western North America, Samantha J. Bock, Morgan M. Malley, Sean Lema

Biological Sciences

The speckled dace Rhinichthys osculus (order Cypriniformes), also known as the carpita pinta, is a small cyprinid minnow native to western North America. Here, we report the sequencing of the full mitochondrial genome (mitogenome) of R. osculus from a male fish collected from the Amargosa River Canyon in eastern California, USA. The assembled mitogenome is 16 658 base pair (bp) nucleotides, and encodes 13 protein-coding genes, and includes both a 12S and a 16S rRNA, 22 tRNAs, and a 985 bp D-loop control region. Mitogenome synteny reflects that of other Ostariophysian fishes with the majority of genes and RNAs encoded …

Wintering North Pacific Black-Legged Kittiwakes Balance Spatial Flexibility And Consistency, Rachael Orben, Rosana Paredes, Daniel Roby, David Irons, Scott A. Shaffer

Faculty Publications, Biological Sciences

Background Marine environments are inherently dynamic, yet marine predators are often long-lived and employ strategies where consistency, individual specialization, routine migrations, and spatial memory are key components to their foraging and life-history strategies. Intrinsic determinates of animal movements are linked to physiological and life-history traits (e.g. sex, colony, experience), while extrinsic influences occur as the result of an animal’s interactions with either other animals or the environment (e.g. prey availability, weather, competition). Knowledge of the factors affecting animal movements is critical to understand energetic bottlenecks and population dynamics. Here, we attempt to understand the interaction of some of these factors …

Ca2+/Calmodulin Regulates Kvβ1.1-Mediated Inactivation Of Voltage-Gated K+ Channels, Sandip M. Swain, Nirakar Sahoo, Sophie Dennhardt, Roland Schönherr, Stefan H. Heinemann

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

A-type K+ channels open on membrane depolarization and undergo subsequent rapid inactivation such that they are ideally suited for fine-tuning the electrical signaling in neurons and muscle cells. Channel inactivation mostly follows the so-called ball-and-chain mechanism, in which the N-terminal structures of either the K+ channel’s α or β subunits occlude the channel pore entry facing the cytosol. Inactivation of Kv1.1 and Kv1.4 channels induced by Kvβ1.1 subunits is profoundly decelerated in response to a rise in the intracellular Ca2+ concentration, thus making the affected channel complexes negative feedback regulators to limit neuronal overexcitation. With electrophysiological and biochemical experiments we …

Loss Of Glycosaminoglycan Receptor Binding After Mosquito Cell Passage Reduces Chikungunya Virus Infectivity, Dhiraj Acharya, Amber M. Paul, John F. Anderson, Faqing Huang, Fengwei Bai

Faculty Publications

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that can cause fever and chronic arthritis in humans. CHIKV that is generated in mosquito or mammalian cells differs in glycosylation patterns of viral proteins, which may affect its replication and virulence. Herein, we compare replication, pathogenicity, and receptor binding of CHIKV generated in Vero cells (mammal) or C6/36 cells (mosquito) through a single passage. We demonstrate that mosquito cell-derived CHIKV (CHIKV_mos) has slower replication than mammalian cell-derived CHIKV (CHIKV_vero), when tested in both human and murine cell lines. Consistent with this, CHIKV_mos infection in both cell lines …

Genus-Wide Assessment Of Bactrurus (Amphipoda: Crangonyctidae) Informs Conservation And Management Of Groundwater Habitats, Matthew L. Niemiller, Steven J. Taylor

National Cave and Karst Management Symposia

No abstract provided.

Karst Wreckage: Subterranean Fauna As Collateral Damage, Julian J. Lewis, Salisa L. Lewis

National Cave and Karst Management Symposia

No abstract provided.

Managing The Spread Of Pseudogymnoascus Destructans And Conserving Bats Threatened By White-Nose Syndrome In North America, Jeremy Coleman, Jonathan D. Reichard, Richard Geboy, Christopher Servheen, Christina Kocer, Mike Armstrong

National Cave and Karst Management Symposia

No abstract provided.

Strip Adaptive Cluster Sampling With Application To Cave Crickets, Kurt Lewis Helf

National Cave and Karst Management Symposia

No abstract provided.

Monitoring In-Cave Resources With Reduced Impact And Increased Quantitative Capacity: Developing Photogrammetry Methodologies For In Cave Environments, Robyn L. Henderek, John R. Wood, Benjamin W. Tobin

National Cave and Karst Management Symposia

No abstract provided.

The Extirpation Of A Population Of The Endangered Illinois Cave Amphipod (Gammarus Acherondytes) By An Exotic Species: The Wednesday Cave Debacle, Julian J. Lewis, Salisa L. Lewis

National Cave and Karst Management Symposia

No abstract provided.

White-Nose Syndrome Response At Mammoth Cave National Park, Rickard S. Toomey

National Cave and Karst Management Symposia

No abstract provided.

Will Remote Sensing Shape The Next Generation Of Species Distribution Models?, Kate S. He, Bethany A. Bradley, Anna F. Cord, Duccio Rocchini, Mao‐Ning Tuanmu, Sebastian Schmidtlein, Woody Turner, Martin Wegmann, Nathalie Pettorelli

Faculty & Staff Research and Creative Activity

Two prominent limitations of species distribution models (SDMs) are spatial biases in existing occurrence data and a lack of spatially explicit predictor variables to fully capture habitat characteristics of species. Can existing and emerging remote sensing technologies meet these challenges and improve future SDMs? We believe so. Novel products derived from multispectral and hyperspectral sensors, as well as future Light Detection and Ranging (LiDAR) and RADAR missions, may play a key role in improving model performance. In this perspective piece, we demonstrate how modern sensors onboard satellites, planes and unmanned aerial vehicles are revolutionizing the way we can detect and …

Catalytic Mechanism Of Mammalian Adenylyl Cyclase: A Computational Investigation, David K. Hahn, Jose R. Tusell, Stephen R. Sprang, Xi Chu

Biological Sciences Faculty Publications

Adenylyl cyclase (AC) catalyzes the synthesis of cyclic AMP, an important intracellular regulatory molecule, from ATP. We propose a catalytic mechanism for class III mammalian AC based on density functional theory calculations. We employ a model of the AC active site derived from a crystal structure of mammalian AC activated by Gα·GTP and forskolin at separate allosteric sites. We compared the calculated activation free energies for 13 possible reaction sequences involving proton transfer, nucleophilic attack, and elimination of pyrophosphate. The proposed most probable mechanism is initiated by deprotonation of 3'OH and water-mediated transfer of the 3'H to the γ-phosphate. Proton …

Synthesis Of Phylogeny And Taxonomy Into A Comprehensive Tree Of Life, Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, H. Dail Laughinghouse Iv, Emily Jane Mctavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams, Karen A. Cranston

Biological Sciences: Faculty Publications

Reconstructing the phylogenetic relationships that unite all line- ages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips— the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. …

Traversing Swanton Road, 21st Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …