Exam 3: Biology

Which of the following is generally true about the path of blood flow through the heart?

Passage Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common heterogeneous disorders, with a reported incidence of 1 in 1,000 people.  The primary pathology is the development of numerous fluid-filled renal cysts that ultimately expand and severely impair kidney function.  By age 60, approximately 50% of patients with ADPKD progress to end-stage renal disease (ESRD) and kidney failure.  Clinical complications include high blood pressure, urinary tract infections, and cysts in other organs such as the liver and pancreas.Approximately 85% of ADPKD cases are caused by mutations in the PKD1 gene, which codes for the protein polycystin-1 (PC1).  The remaining 15% of cases are caused by mutations in the PKD2 gene, which codes for the protein polycystin-2 (PC2).  The PC2 protein functions as a mechanically activated calcium (Ca²⁺) channel in ciliated renal epithelial cells.  PC1 and PC2 interact via their C-terminal cytoplasmic tails to form a heteromer that modulates intracellular calcium homeostasis.  Disruption of calcium signaling as a result of mutations in either PKD1 or PKD2 is associated with increased cell growth and cyst formation in ADPKD patients.To identify individuals with mutations in PKD1 and PKD2, researchers analyzed phenotypic and genetic data from patients with established renal disease, as shown in Table 1.Table 1  Comparison of Renal Disease Onset and Symptom Severity in Various Patient Groups Next, researchers examined how phenotypic disease severity was affected by both the position of the mutations in PKD1 (5′ or 3′ end) and the type of mutation in PKD1 or PKD2.  In Figure 1, disease severity is given as the cumulative probability of renal survival as a function of age. Figure 1  Probability of maintaining healthy kidney physiology as a function of age, analyzed by mutation type and position Adapted from Cornec-le gall E, Audrézet MP, Chen JM, et al. J Am Soc Nephrol. 2013;24(6):1006-13. -Which set of amino acids would most likely be found in the pore of the channel formed by PC2?  (Assume the amino acids are at physiological pH.)

During a parasitic infection, which of the following would most likely be responsible for phagocytosis of organisms and the release of histamine, respectively?

Passage Bone remodeling is the continuous, microscopic process by which bone tissue throughout the body is resorbed and re-deposited.  Proper regulation of bone remodeling is necessary to maintain bone strength and prevent the onset of conditions of fragile bone such as osteoporosis.  Patients with such conditions have increased fracture risk and generally exhibit decreased activity of osteoblasts (bone-depositing cells), leading to reduced bone density and weakening of the bone matrix.  However, some cases can occur due to overactive osteoclasts (multinucleated cells that mediate bone resorption).  Osteoclasts resorb bone by secreting proteolytic enzymes and acids into the adjacent extracellular space.  These enzymes degrade the organic matrix of bone, and the acid causes the dissolution and release of the mineral components of bone, such as calcium, potassium, and magnesium.  Generally, less than 1% of adult bone is occupied by active osteoclasts.Osteoclast differentiation and activation is thought to be related to the RANK/RANKL signaling pathway.  RANKL, expressed as a membrane-bound or secreted protein, serves as the ligand for RANK, a transmembrane receptor.  In bone tissue, RANK is expressed by precursors of mature osteoclasts, also known as osteoclast progenitor cells (OPCs).  RANKL is expressed by osteoblasts adjacent to OPCs, and the binding of RANKL to RANK in these neighboring cells causes downstream effects through recruitment of TRAF6, an intracellular protein.  TRAF6 activates multiple downstream signaling cascades, but only four of these directly mediate the development of mature osteoclasts from OPCs.  In one of the four pathways, the transcription factor NF-kB is activated, which leads to increased expression of the proto-oncogene c-Fos.  Subsequently, c-Fos interacts with another transcription factor known as NFATc to promote the expression of genes related to osteoclast-specific development and function in OPCs (Figure 1). Figure 1  RANK/RANKL signaling induces differentiation of OPCs into osteoclasts -A group of scientists hypothesized that elevated RANKL signaling contributes to the decrease in bone density associated with osteoporosis.  To confirm their hypothesis, they collected bone tissue samples from patients with the disease and compared them to healthy controls.  Given this information, all of the following experimental observations would support their hypothesis EXCEPT:

Passage Abnormal blood lipid levels play a significant role in the development of coronary artery disease (CAD).  The discovery of genomic variations that confer a protective effect against CAD has prompted investigations into the biological impact of these protective alleles.  Researchers have observed that specific single-base variations in the ANGPTL4 gene are common among patients with a low occurrence of CAD.  ANGPTL4 is located on chromosome 19 and codes for angiopoietin-like 4, a multifunctional glycosylated protein.One of the functions of angiopoietin-like 4 is the regulation of lipid metabolism.  The N-terminal domain of angiopoietin-like 4 induces a conformational change in the enzyme lipoprotein lipase (LPL), forcing the LPL homodimer to dissociate into two inactive 225-residue monomers.  LPL functions on the surface of vascular endothelial cells and degrades the triglycerides of chylomicrons and very-low-density lipoproteins (VLDLs) in the blood.  Elevated triglyceride levels have been correlated with increased CAD risk.To identify common loss-of-function mutations in ANGPTL4, DNA samples from 43,000 individuals with CAD and 78,000 individuals without CAD were genotyped.  A detailed analysis of ANGPTL4 genomic variants was performed, and the results of individuals without CAD were mapped in Figure 1.  The lipid profiles of ANGPTL4 mutation noncarriers were also compared to those of mutation carriers (Figure 2). Figure 1  Loss-of-function mutations observed in ANGPTL4 in participants without CAD  (Note:  * = mutation resulting in a truncated protein; † = substitution of a cytosine for its complementary base.) Figure 2  Mean plasma lipid levels for ANGPTL4 mutation carriers and noncarriers (Note:  LDL = low-density lipoprotein; HDL = high-density lipoprotein; error bars = standard deviation.)To further analyze the effect of ANGPTL4 on blood lipid levels, ANGPTL4 knockout mice and mice that constitutively express ANGPTL4 were created.  Researchers hypothesized that two of the four biological profiles shown in Table 1 would be observed in these mice.Table 1  Predicted Biological Profiles of ANGPTL4 Mouse Models -The knockout mouse model and the constitutively active mouse model of ANGPTL4 are best represented by:

Renal studies in mice have revealed that a mutation in various sodium transporters causes impaired active transport of NaCl from the filtrate within the loop of Henle to the medulla.  If mice with wild-type sodium transporters were compared to mice with the mutated sodium transporters, the mutant mice would likely exhibit all of the following EXCEPT:

Passage Viruses are known as obligate intracellular parasites because they cannot reproduce independently (outside of a host cell).  Viral genomes (RNA or DNA) are enclosed by a protein shell known as the capsid.  Some viruses, known as enveloped viruses, have an additional phospholipid bilayer that fully envelops the capsid.  Viruses that lack this outermost phospholipid covering are labeled non-enveloped.  The entry of either enveloped or nonenveloped viruses into a host cell enables the production of viral proteins and the subsequent assembly of viral progeny.Immune cells (B and T cells) protect host organisms against viral infections by recognizing viral particles (antigens) as foreign.  In response to the recognition of foreign particles, antigen-presenting cells display cleaved antigens (also known as antigen fragments) on their surface, which enable the activation of other immune cells that stimulate an immune response, including the production of neutralizing antibodies.An example of an infectious disease is viral hepatitis (inflammation of the liver), which can be caused by any one of five distinct hepatitis viruses (A-E) that infect hepatocytes (liver cells).  HAV, HCV, and HEV contain positive-sense, single-stranded RNA (+ssRNA) as genetic material.  In contrast, HBV has a partially double-stranded circular DNA genome.  HDV is unique because it has a negative-sense, single-stranded RNA (−ssRNA) genome.Researchers hypothesized that synthetic antibodies could be used to treat viral hepatitis in patients with compromised immune systems.  Fluorescent antibodies, designed to bind the capsid proteins of the five hepatitis viruses, were added to separate wells containing each type of virus.  The fluorescence assay that was performed detected only bound antibodies in media with HAV or HEV. Adapted from Shin EC, Sung PS, Park SH. Immune responses and immunopathology in acute and chronic viral hepatitis. Nat Rev Immunol. 2016;16(8):509-23. -Physicians researching a global hepatitis outbreak discover a new strain of hepatitis (HXV) by analyzing chromosomal DNA of patient's liver cells.  They found that HXV has a +ssRNA genome and replicates through DNA intermediates.  What characteristic best describes the new hepatitis virus?

During a nutrition study, a participant consumes five times the physician-recommended amount of food but is unable to sufficiently absorb nutrients.  Given this information, this participant would be LEAST likely to exhibit which of the following conditions?

Passage The Bloom syndrome helicase (BLM) transcript is catalytically inactive in Bloom syndrome (BS), a genetic disorder that leads to genomic instability characterized by excessive somatic recombination events.  Research studies have shown that BLM may be involved in DNA synthesis repair of stalled replication forks during replication stress (arrest).  To investigate this further, an experiment was conducted using cell lines derived from a patient with BS.  One set of cells differed only by BLM status:  PSNF5 (BLM⁺, vector with BLM cDNA transfected) and PSNG13 (BLM⁻, empty vector transfected).  Additional mutations, BLM-K695T and BLM-T99A, were studied in stable transfected cells.The nucleoside analogs iododeoxyuridine (IdU) and chlorodeoxyuridine (CldU) were used to label and track genomic regions of active replication.  Cells were initially treated with IdU for 15 minutes.  Subsequently, either 4 mM of hydroxyurea (HU) or 30 µM of aphidicolin (Aph) were used to induce replication stress for 4 hours, after which cells were treated with CldU for 85 minutes to assess replication recovery.  Cells were mounted on microscope slides, lysed to isolate chromosome fibers, and then fixed on the slides.  Sites of IdU and CldU incorporation into the growing DNA strand were then detected by immunostaining the isolated chromosome fibers with analog-specific, fluorescent-coupled antibodies.  Replication activity was visualized via microscopy and measured. Figure 1  (A) Experimental protocol and (B) fluorescent imaging of a microscope slide showing incorporation of IdU (black lines) and CldU (gray lines) into DNA fibers isolated from a group of BLM⁺ and BLM⁻ cells, with single fibers depicted in each row Figure 2  Replication fork recovery in cells expressing BLM⁺, BLM⁻, and the mutation BLM-K695T (antagonistic to wild-type) Figure 3  New sites of replication in cells expressing BLM⁺, BLM⁻, and the mutation BLM-T99A (T99 phosphorylated after replication arrest) Adapted from Davies SL, North PS, Dart A, Lakin ND, Hickson ID. Mol Cell Biol. 2004;24(3):1279-91. -After Aph treatment, replication fork recovery in PSNF5 and PSNG13 cells was analyzed as a function of time.  Which of the following conclusions explains the data shown in the graph below?

Researchers are screening bacterial chromosomes for mutations affecting protein function.  After using DNA sequencing analysis and analyzing the gel electrophoresis results, they identify a sequence with a single point mutation in which the fourth nucleotide has been changed from adenine to cytosine.  The sequence is shown below.5′-TTACG-3′Which of the following gel electrophoresis diagrams obtained from DNA sequencing analysis represents this sequence?

Passage The adrenal glands are divided into two anatomically distinct regions, the adrenal medulla and the adrenal cortex.  The adrenal medulla is a collection of irregularly shaped cells located in the interior portion of each adrenal gland.  In response to changing serum levels of corticosteroid hormones, medullary cells synthesize and secrete the catecholamines norepinephrine and epinephrine.  Norepinephrine and epinephrine are water-soluble compounds, and their actual secretion into the bloodstream is stimulated by acetylcholine (ACh)-mediated signaling in the sympathetic component of the autonomic nervous system.  Figure 1 shows the enzyme-mediated synthesis of norepinephrine and epinephrine. Figure 1The adrenal cortex is the outer portion of the adrenal gland and is composed of cells that synthesize and secrete lipophilic hormones derived from cholesterol.  Hormones produced by the adrenal cortex include the principal glucocorticoid hormone (cortisol) and the mineralocorticoid hormone (aldosterone).The hypothalamus and pituitary gland regulate and control the endocrine functions of the adrenal cortex (Figure 2).  Secretion of corticotrophin-releasing hormone (CRH) from the hypothalamus promotes the synthesis and release of adrenocorticotrophic hormone (ACTH) by the pituitary gland.  ACTH acts on adrenal cortex cells to promote the growth of cortical tissue and to increase the synthesis and secretion of glucocorticoids.  In addition to its body-wide functions as the principal stress hormone, cortisol also regulates adrenal activity by inhibiting CRH release from the hypothalamus and ACTH release from the pituitary. Figure 2 -For individuals who exhibit insufficient hormone production by the adrenal cortex, ACTH is sometimes administered as a treatment option.  Clinicians have reported that most patients fail to respond to this treatment with ACTH.  The most likely reason for this outcome is that nonresponsive patients:

A physician measures the arterial blood pressure of a patient while she is resting and again while she is running on a treadmill.  The results of these blood pressure tests are given in the table below. Given this data, was arterial blood pressure during heart contraction higher while the patient was resting or while she was running?

A subset of aggressive cancers has a relatively high growth rate, leading to the formation of large tumors.  An effective drug against fast-growing tumors would most likely NOT target which stage of the cell cycle?

Passage Beta-thalassemia is a blood disorder caused by reduced production of the β-globin subunit of hemoglobin.  The erythrocytes in patients with beta-thalassemia are abnormally small, lack sufficient functional hemoglobin, and are decreased in number.  These individuals require lifelong blood transfusions to correct their erythrocyte shortage.  Each unit of blood transfused contains many milligrams of iron and, consequently, blood iron levels increase due to repeated transfusions.  The excess iron is then continuously deposited in the organs, leading to organ damage.Transferrin (Tf) is a protein that binds free iron in the blood and plays a key role in erythropoiesis, which requires uptake of iron from the blood in a process facilitated by Tf and its cell surface receptor (TfR).  Iron-bound Tf, known as holotransferrin (holoTf), binds TfR to form a complex that is brought into the developing erythrocyte in an endosome.  Acidification of the endosome triggers a conformational change in holoTf, which allows the release of free iron into the cell and the recycling of the remaining complex components to the cell surface.  Non-iron-bound Tf is referred to as apotransferrin (apoTf), and due to its iron-binding capability, researchers believe that apoTf injections may help prevent deposition of excess iron in the organs of patients with beta-thalassemia.To investigate the effect of apoTf administration in a mouse model of beta-thalassemia, mice homozygous for an inactivating deletion in the murine β-globin gene (Hbb^th−3/Hbb^th−3) were given blood transfusions followed by apoTf injection.  Measurements of non-transferrin-bound iron in the blood (NTBI), plasma holoTf, and urinary holoTf were taken immediately and at 15 days post-injection.  Results revealed that NTBI decreased over the tested period.  Experimenters hypothesized that apoTf mediated certain regulatory changes that reduced NTBI in Hbb^th−3/Hbb^th−3 mice by increasing urinary holoTf excretion. -Individuals with beta-thalassemia are at risk for developing an enlarged spleen.  The resulting impairment of spleen function in these individuals would NOT affect:

Passage Domestic pigs have been used as valuable preclinical models for scientific research due to their numerous anatomical, developmental, and physiological similarities to humans.  For example, oogenesis and embryonic development in pigs are remarkably similar to the human processes and have facilitated the study of impaired fertilization due to decreased oocyte competence (quality).Researchers have hypothesized that early termination of embryo development can arise from low mitochondrial DNA (mtDNA) copy number.  Because mtDNA replication and reduction events have been extensively mapped in pigs, oocytes and sperm were isolated from their respective porcine gonads to test this hypothesis.Experiment 1To evaluate the developmental competence of porcine oocytes, researchers first measured the activity of glucose-6-phosphate dehydrogenase (G6PD), an enzyme that is downregulated as the oocyte matures.  The oocytes were stained with Brilliant Cresyl Blue (BCB), a nontoxic blue dye that is converted to a colorless compound by G6PD.  After 90 minutes of staining, oocytes were divided into two groups: one contained oocytes with colorless cytoplasm (BCB⁻) and the other contained oocytes with blue cytoplasm (BCB⁺).  Gene expression profiles were compared to evaluate the number of oocytes in the BCB⁺ and BCB⁻ groups that had developed to metaphase II.Experiment 2BCB⁺ and BCB⁻ oocytes underwent in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), or supplementation with homogeneous mitochondria and ICSI (mICSI).  During IVF, an isolated oocyte was placed in a well plate and incubated with sperm at 39 C for 4 hours.  In ICSI, a single sperm was selected and injected directly into the oocyte.Table 1  Developmental Rates for BCB⁺ and BCB⁻ Oocytes Fertilized Subjected to IVF, ICSI, or mICSI Adapted from Cagnone GL, Tsai TS, Makanji Y, et al. Sci Rep. 2016;6:23229. -All of the following findings in sperm would cause lower fertilization rates in IVF EXCEPT:

Passage Domestic pigs have been used as valuable preclinical models for scientific research due to their numerous anatomical, developmental, and physiological similarities to humans.  For example, oogenesis and embryonic development in pigs are remarkably similar to the human processes and have facilitated the study of impaired fertilization due to decreased oocyte competence (quality).Researchers have hypothesized that early termination of embryo development can arise from low mitochondrial DNA (mtDNA) copy number.  Because mtDNA replication and reduction events have been extensively mapped in pigs, oocytes and sperm were isolated from their respective porcine gonads to test this hypothesis.Experiment 1To evaluate the developmental competence of porcine oocytes, researchers first measured the activity of glucose-6-phosphate dehydrogenase (G6PD), an enzyme that is downregulated as the oocyte matures.  The oocytes were stained with Brilliant Cresyl Blue (BCB), a nontoxic blue dye that is converted to a colorless compound by G6PD.  After 90 minutes of staining, oocytes were divided into two groups: one contained oocytes with colorless cytoplasm (BCB⁻) and the other contained oocytes with blue cytoplasm (BCB⁺).  Gene expression profiles were compared to evaluate the number of oocytes in the BCB⁺ and BCB⁻ groups that had developed to metaphase II.Experiment 2BCB⁺ and BCB⁻ oocytes underwent in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), or supplementation with homogeneous mitochondria and ICSI (mICSI).  During IVF, an isolated oocyte was placed in a well plate and incubated with sperm at 39 C for 4 hours.  In ICSI, a single sperm was selected and injected directly into the oocyte.Table 1  Developmental Rates for BCB⁺ and BCB⁻ Oocytes Fertilized Subjected to IVF, ICSI, or mICSI Adapted from Cagnone GL, Tsai TS, Makanji Y, et al. Sci Rep. 2016;6:23229. -Which of the following statements best describes a BCB⁺ oocyte that is arrested in metaphase II?

Passage Within the Actinopterygii (bony fish) lineage, marine teleosts (bony fish with mobile jaws) live in an aquatic environment where there is a higher external concentration of salt and a lower concentration of water relative to the internal concentrations.  Owing to these conditions, salt ions tend to diffuse into the teleost through its skin, whereas water molecules within the organism osmotically traverse the opposite path.Irrespective of lineage, many fish species actively assess their environment and regulate their internal concentration of fluids and electrolytes via a homeostatic process known as osmoregulation.  Teleosts with either glomerular kidneys (eg, eels, sculpin) or aglomerular kidneys that are purely tubular (eg, goosefish, toadfish) have served as experimental subjects for the study of marine teleost osmoregulation.  Analyzing the ionic (ie, Na⁺, Cl⁻, Mg²⁺, SO₄²⁻) concentration of intestinal fluids, urine, and plasma in each species led to the discovery that the renal tubule of the goosefish has both excretory and reabsorptive functions.Scientists have concluded that marine teleost osmoregulation involves the ingestion of seawater, retrieval of NaCl and water from the intestine, and primary excretion of divalent ions via urine and monovalent ions through the gills (thin barriers between the organism's blood and the aquatic environment).In an experiment to further study osmoregulatory mechanisms, researchers emptied the gut of an eel and sealed the anus to prevent fluid loss.  The eel was transported into seawater that had been treated with the volume marker phenol red.  After 20 hours, the eel's gut contained 2.3 mL of fluid but showed a phenol red concentration equivalent to 12.3 mL of ingested seawater.  Researchers found that the eel lost 2.3 g of weight due to urine output.  They ultimately reported that the eel had lost all the seawater it absorbed through the gut via various mechanisms. -Based on the passage, to confirm that the inorganic composition of marine teleost urine is independent of glomerular function, researchers would most likely have to discover:

Passage Obesity is a condition that affects over 30% of adults in the United States and is associated with comorbidities such as type 2 diabetes mellitus, heart disease, and cancer.  For individuals with clinically severe obesity, defined as having a body mass index above 40 kg/m², lifestyle interventions may produce insufficient weight reduction.  Weight loss surgery, such as Roux-en-Y gastric bypass (RYGB), has proved to be the most effective clinical intervention for facilitating massive and immediate weight loss in clinically obese patients.In RYGB, the stomach is first divided into a small gastric pouch and a distal gastric remnant, which remains attached to the duodenum.  Next, the jejunum is transected and its lower section is connected to the newly created gastric pouch to form the alimentary limb.  This connection is typically created with surgical staples.  The formation of the alimentary limb allows ingested food to bypass the region composed of the distal gastric remnant, the duodenum, and the upper jejunum; collectively termed the biliopancreatic limb.  Finally, the lumen of the upper jejunum is reconnected to the lumen of the lower jejunum to allow enzymes and compounds to flow freely from the biliopancreatic limb into the alimentary limb. Figure 1  RYGB surgically divides the digestive tract into the alimentary limb and the biliopancreatic limb, which then merge into the common limb.RYGB facilitates weight loss by reducing the functional volume of the stomach and altering intestinal anatomy to induce nutrient malabsorption.  However, the procedure is associated with several complications, such as steatorrhea, or fatty stools, due to disruption of lipid digestion.  Animal studies also suggest that RYGB promotes the growth of weight loss-inducing gut bacteria.  Researchers have found that transplanting gut microbiota of obese postoperative RYGB mice into nonoperated, obese mice lacking gut flora may reproduce the therapeutic effects of RYGB in transplant-recipient mice. Adapted from Bächler T, Le roux CW, Bueter M. How do patients' clinical phenotype and the physiological mechanisms of the operations impact the choice of bariatric procedure?. Clin Exp Gastroenterol. 2016;9:181-9. -Which organ synthesizes a compound that facilitates the mechanical digestion of lipids?

A pathogen identified in a patient's blood sample is found to lack a phospholipid bilayer.  Therefore, any medications used to treat the disease caused by this pathogen would most likely be classified as:

Passage Quantitative fluorescence recovery after photobleaching (FRAP) is used to study the movement of molecules in live cells.  During FRAP, the fluorescence of a green fluorescent protein (GFP)-tagged molecule is first measured and then photodestroyed in targeted cell regions.  Researchers then assess the time course for fluorescence recovery, which is an indicator of molecular mobility of the GFP-tagged protein into the photodestroyed region.  The average time required to recover 80% of the pre-bleach fluorescence of protein histone 1 (H1) fused to GFP (H1-GFP) in the photodestroyed region is given as t80.FRAP was used to analyze the mobility of the architectural H1 alone and in the presence of high-mobility group (HMG) proteins.  HMG proteins are dynamic modifiers that have been shown to have opposite effects but similar binding sites on chromatin structure. Figure 1  Unique chromatin binding motifs of HMG proteinsDuring analysis, HMGA1 and HMGB1 were microinjected into the cytoplasm of mouse embryonic fibroblast cells expressing H1-GFP.  FRAP was performed on euchromatin and heterochromatin.  Euchromatin and heterochromatin domains were identified as regions weakly and strongly stained by H1-GFP, respectively.  The relative intensity of H1-GFP fluorescence in euchromatin and heterochromatin of uninjected and injected cells was assessed, and t80 results are shown in Table 1.Table 1  Effect of HMGB1 and HMGA1 on H1-GFP Mobility Adapted from Catez F, Yang H, Tracey KJ, Reeves R, Misteli T, Bustin M. Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin. Mol Cell Biol. 2004;24(10):4321-8. -A recent study of a model organism showed that HMG-5, another member of the HMG family, mainly localized to the end of chromosomes.  The site of HMG-5 localization would correspond to regions in humans that: