nirantk/geneticsQA-train huggingface dataset:
Question: What are the effects of BMAL1 deficiency?

Context:
BMAL1 deficiency is associated with premature aging and reduced lifespan
BMAL1 deficiency leads to development of stress induced senescence in vivo.
 Down-regulation of Bmal1 accelerates the development of tumours 
BMAL1 deficiency results in premature aging in mice
BMAL1 deficiency disrupts circadian oscillation in gene expression and reactive oxygen species homeostasis in the brain,
We demonstrate that attenuation of Bmal1 function resulted in down-regulation of genes in the canonical Wnt pathway, known to suppress adipogenesis. 

Answer: BMAL1 deficiency is associated with premature aging and reduced lifespan and BMAL1 deficiency leads to development of stress induced senescence in vivo. Down-regulation of Bmal1 also accelerates the development of tumours, adipogenesis.
Question: Is it possible to visualize subtahalamic nucleus by using transcranial ultrasound?

Context:
After measuring thermal effects of TCS and imaging artefact sizes of DBS lead using a skull phantom, we prospectively enrolled 34 patients with DBS of globus pallidus internus, ventro-intermediate thalamic or subthalamic nucleus. TCS had no influence on lead temperature, electrical parameters of DBS device or clinical state of patients. TCS measures of lead coordinates agreed with MRI measures in anterior-posterior and medial-lateral axis. Lead dislocation requiring reinsertion was reliably detected.
TCS may therefore become a first-choice modality to monitor lead location.
Two pilot studies have demonstrated that the intraoperative visualization with TCS and the TCS-assisted insertion of deep-brain stimulation (DBS) electrodes into the subthalamic nucleus and the globus pallidus interna are feasible and safe provided there is exact knowledge on the extent of electrode TCS imaging artifacts. 
Peroperative transcranial sonography for electrode placement into the targeted subthalamic nucleus of patients with Parkinson disease: technical note
The correct anatomic position of the electrode tip could be indirectly assessed thanks to the topographic relationship of the STN with the hyperechogenic substantia nigra and the nucleus ruber.
CONCLUSIONS: Transcranial sonography is easily feasible during stereotactic surgery. In combination with the clinical effects of electrostimulation on the symptoms of Parkinson's disease and with stereotactic x-ray images, it enables the assessment and the documentation of the correct position of implanted STN electrodes in real time.
After measuring thermal effects of TCS and imaging artefact sizes of DBS lead using a skull phantom, we prospectively enrolled 34 patients with DBS of globus pallidus internus, ventro-intermediate thalamic or subthalamic nucleus
Two pilot studies have demonstrated that the intraoperative visualization with TCS and the TCS-assisted insertion of deep-brain stimulation (DBS) electrodes into the subthalamic nucleus and the globus pallidus interna are feasible and safe provided there is exact knowledge on the extent of electrode TCS imaging artifacts

Answer: Yes, it has been shown that it is possible to visualize subtahalamic nucleus by using transcranial ultrasound. Transcranial ultrasound is safe and reliable method that can be employed to monitor lead location and intraoperative visualization of deep-brain stimulation (DBS) electrodes.
Exact answer: yes
Question: Which trancription factor activates the betalain pathway?

Context:
The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway.
Some putative MYB, bHLH, and environmental stress-responsive transcription factor binding sites were detected in the PaDOD1 and PaDOD2 promoter regions.

Answer: The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway.
Exact answer: The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway.
Question: List kinases that phosphorylates the protein Bora.

Context:
During cell division Bora becomes multiply phosphorylated by a variety of cell cycle kinases, including Aurora A and Plk1, albeit at distinctive sites.
Likewise, we find that phosphorylation of Bora by Cdk1 promotes phosphorylation of human Plk1 by Aurora A suggesting that this mechanism is conserved in humans. 
we show that the master mitotic kinase Cdk1 contributes to Plk1 activation through SPAT-1/Bora phosphorylation
the potential role of Bora phosphorylation by Cdk1 in this process
phosphorylation of Bora on the Cdk consensus site T52 blocks Bora degradation.
Here, we used the LC-MS/MS phosphopeptide mapping assay to identify 13 in vivo hBora phosphorylation sites and characterized that GSK3β can interact with hBora and phosphorylate hBora at Ser274 and Ser278.

Answer: During cell division Bora becomes multiply phosphorylated by a variety of cell cycle kinases, including Aurora A and Plk1, and GSK3β and Cdk1 albeit at distinctive sites.
Exact answer: Cdk1, Plk1, Aurora A, GSK3β
Question: What is Tarlov Cyst?

Context:
She underwent ultrasound, CT, and eventually MRI evaluations that led to the diagnosis of a giant (6.7 × 6.4 × 6.6 cm) Tarlov cyst originating from the right S-2 nerve root sleeve/sacral foramen with intrapelvic extension.
We report here a case of multiloculated disseminated perineural or Tarlov cysts (TCs). 
TCs are typically benign, asymptomatic lesions that can simply be monitored.
Tarlov cyst syndrome is a rare, often asymptomatic disorder, characterised by isolated or multiple nerve-root cysts, usually occurring in the sacral spine, near the dorsal root ganglion, between the perineurium and endoneurium. 
Perineural (Tarlov) cysts are most often found in the sacral region and are rare in the cervical spine. 
A case of symptomatic cervical perineural (Tarlov) cyst: clinical manifestation and management.
Tarlov cysts or spinal perineurial cysts are uncommon lesions.
Tarlov cyst syndrome is a rare, often asymptomatic disorder, characterised by isolated or multiple nerve-root cysts, usually occurring in the sacral spine, near the dorsal root ganglion, between the perineurium and endoneurium.
Symptomatic sacral perineurial (Tarlov) cysts.
Subsequent MRI and CT myelography demonstrated the nature of the photopenic area as secondary to vertebral erosion by sacral perineurial cyst (Tarlov cyst).
Tarlov cysts are sacral perineural cysts. This case report describes the clinical course after biopsy of a very large Tarlov cyst via laparoscopy, which was thought preoperatively to be an adnexal mass.
Subsequent MRI and CT myelography demonstrated the nature of the photopenic area as secondary to vertebral erosion by sacral perineurial cyst (Tarlov cyst).
A spinal MRI scan was then performed and revealed a sacral fracture which drained into an unknown perineurial cyst (Tarlov cyst).
Tarlov or perineurial cysts are lesions of the nerve root most often found in the sacral region. Although there is agreement that asymptomatic Tarlov cysts should be followed, it is still debated whether patients with symptomatic Tarlov cysts should be treated surgically.
Tarlov cysts (sacral perineural cysts) are nerve root cysts found most commonly in the sacral roots,
Tarlov cysts or spinal perineurial cysts are uncommon lesions.
Sacral perineurial (Tarlov) cysts are rare lesions.

Answer: Tarlov or perineural cysts are nerve root cysts found most commonly at the sacral spine level arising between covering layers of the perineurium and the endoneurium near the dorsal root ganglion and are usually asymptomatic.
Question: What type of genome, (RNA or DNA, double stranded single stranded) is found in the the virus that causes blue tongue disease?

Context:
Bluetongue virus (BTV) genome contains ten double-stranded RNA segments

Answer: The Bluetongue virus (BTV) genome contains ten double-stranded RNA segments.
Bluetongue virus (BTV) genome contains ten double-stranded RNA segments. 
Bluetongue virus (BTV) genome contains ten double-stranded RNA segments.
Bluetongue virus (BTV) genome contains ten double-stranded RNA segments
bluetongue virus (btv) genome contains ten double-stranded rna segments.
Exact answer: double stranded, segmented RNA
Question: What is the implication of histone lysine methylation in medulloblastoma?

Context:
Through targeted re-sequencing, we identified mutations of MLL2 in 8 % (14/175) of MBs, the majority of which were loss of function. Notably, we also report mutations affecting the MLL2-binding partner KDM6A, in 4 % (7/175) of tumors. While MLL2 mutations were independent of age, gender, histological subtype, M-stage or molecular subgroup, KDM6A mutations were most commonly identified in Group 4 MBs, and were mutually exclusive with MLL2 mutations. Immunohistochemical staining for H3K4me3 and H3K27me3, the chromatin effectors of MLL2 and KDM6A activity, respectively, demonstrated alterations of the histone code in 24 % (53/220) of MBs across all subgroups. Correlating these MLL2- and KDM6A-driven histone marks with prognosis, we identified populations of MB with improved (K4+/K27-) and dismal (K4-/K27-) outcomes, observed primarily within Group 3 and 4 MBs
we identified previously unknown amplifications and homozygous deletions, including recurrent, mutually exclusive, highly focal genetic events in genes targeting histone lysine methylation, particularly that of histone 3, lysine 9 (H3K9). Post-translational modification of histone proteins is critical for regulation of gene expression, can participate in determination of stem cell fates and has been implicated in carcinogenesis. Consistent with our genetic data, restoration of expression of genes controlling H3K9 methylation greatly diminishes proliferation of medulloblastoma in vitro
Copy number aberrations of genes with critical roles in writing, reading, removing and blocking the state of histone lysine methylation, particularly at H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma.
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma.
Copy number aberrations of genes with critical roles in writing, reading, removing and blocking the state of histone lysine methylation, particularly at H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma.
Recent studies showed frequent mutations in histone H3 lysine 27 (H3K27) demethylases in medulloblastomas of Group 3 and Group 4, suggesting a role for H3K27 methylation in these tumors.

Answer: Aberrant patterns of H3K4, H3K9, and H3K27 histone lysine methylation were shown to result in histone code alterations, which induce changes in gene expression, and affect the proliferation rate of cells in medulloblastoma.
Question: Which biomarker is widely used in the diagnosis of Ewing sarcoma?

Context:
half of B-LBL patients are negative for CD45 (leucocyte common antigen, LCA), a widely used marker for the diagnosis of lymphoma, and a significant portion express CD99, a marker for Ewing's sarcoma (ES) or primitive neuroectodermal tumor (PNET)
Moreover, half of B-LBL patients are negative for CD45 (leucocyte common antigen, LCA), a widely used marker for the diagnosis of lymphoma, and a significant portion express CD99, a marker for Ewing's sarcoma (ES) or primitive neuroectodermal tumor (PNET)

Answer: CD99 is a hallmark marker for Ewing sarcoma and primitive neuroectodermal tumors.
Exact answer: CD99
Question: Which disease is linked to mutations within BRAG1?

Context:
Mutations in BRAG1 have been identified in families with X-linked intellectual disability (XLID)

Answer: Mutations in BRAG1 have been identified in families with X-linked intellectual disability (XLID).
Exact answer: X-linked intellectual disability
Question: Which methyl-CpG-binding protein when mutant becomes the hallmark for Rett syndrome?

Context:
Rett syndrome (RTT) results from loss-of-function mutations in the gene encoding the methyl-CpG-binding protein 2 (MeCP2) and is characterized by abnormal motor, respiratory and autonomic control, cognitive impairment, autistic-like behaviors and increased risk of seizures. 
Rett syndrome (RTT) is an autism spectrum disorder caused by mutation in the gene encoding methyl CpG binding protein 2 (MECP2).
Severely arrhythmic breathing is a hallmark of Rett syndrome (RTT) and profoundly affects quality of life for patients and their families. The last decade has seen the identification of the disease-causing gene, methyl-CpG-binding protein 2 (Mecp2) and the development of mouse models that phenocopy many aspects of the human syndrome, including breathing dysfunction.
Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder that manifests in females, typically after the first year of life.
It was recently discovered that RTT is caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene. MECP2 assists in the transcriptional silencing process via DNA methylation; we hypothesize that disruption of this gene alters the normal developmental expression of various other genes, some of which must account for the peculiar neurologic phenotype of RTT.
Molecular studies have identified MECP2 mutations in up to 80% of classic RTT patients; mutation type has some effect on the phenotypic manifestation of RTT, but the pattern of X inactivation seems to determine phenotypic severity.

Answer: Rett syndrome (RTT) was shown to be caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene, with molecular studies identifying MECP2 mutations in up to 80% of classic RTT patients. MECP2 protein was found to assist in the transcriptional silencing process via DNA methylation. We therefore hypothesize that disruption of this gene alters the normal developmental expression of various other genes, some of which must account for the peculiar neurologic phenotype of RTT.
Exact answer: Methyl-CpG-binding protein 2 (MECP2)
Question: Are cutaneous porphyrias inherited with a recessive pattern?

Context:
Five of the porphyrias are low-penetrance autosomal dominant conditions in which clinical expression results from additional factors that act by increasing demand for haem or by causing an additional decrease in enzyme activity or by a combination of these effects
Molecular mechanisms of dominant expression in porphyria.
Variegate porphyria (VP) is an autosomal-dominant disorder that is caused by inheritance of a partial deficiency of the enzyme protoporphyrinogen oxidase (EC 1.3.3.4). It is characterized by cutaneous photosensitivity and/or various neurological manifestations. 
The acute porphyrias constitute a group of metabolic disorders engaging enzymes in the haem synthetic chain and generally following dominant inheritance patterns.

Answer: No, cutaneous porphyrias are inherited in a dominant (not recessive) pattern.
Exact answer: no
Question: Which is the treatment strategy followed in spinocerebellar ataxia type 3 for CAG removal?

Context:
Ataxin-3 protein modification as a treatment strategy for spinocerebellar ataxia type 3: removal of the CAG containing exon
Spinocerebellar ataxia type 3 is caused by a polyglutamine expansion in the ataxin-3 protein, resulting in gain of toxic function of the mutant protein. The expanded glutamine stretch in the protein is the result of a CAG triplet repeat expansion in the penultimate exon of the ATXN3 gene
we propose a novel protein modification approach to reduce mutant ataxin-3 toxicity by removing the toxic polyglutamine repeat from the ataxin-3 protein through antisense oligonucleotide-mediated exon skipping while maintaining important wild type functions of the protein
exon skipping may be a novel therapeutic approach to reduce polyglutamine-induced toxicity in spinocerebellar ataxia type 3
Ataxin-3 protein modification as a treatment strategy for spinocerebellar ataxia type 3: removal of the CAG containing exon.
Ataxin-3 protein modification as a treatment strategy for spinocerebellar ataxia type 3: removal of the CAG containing exon.

Answer: The novel treatment strategy proposed for treatment of Spinocerebellar ataxia type 3 is the removal of the toxic polyglutamine repeat from the ataxin-3 protein through antisense oligonucleotide-mediated exon skipping while maintaining important wild type functions of the protein.
Question: What can Nothobranchius furzeri be used as a model system for?

Context:
The short-lived annual fish Nothobranchius furzeri shows extremely short captive life span and accelerated expression of age markers, making it an interesting model system to investigate the effects of experimental manipulations on longevity and age-related pathologies.
Owing to large differences in aging phenotypes in different lines, N. furzeri could represent a model system for studying the genetic control of life-history traits in natural populations.
It is very close to the Japanese Medaka, and close to the pufferfishes and stickleback and might represent a very useful model for comparative genomics of aging.
In the last three years, N. furzeri has moved from biological curiosity to a promising model system for drug validation.
 This result identifies resveratrol as the first molecule which consistently retards aging in organisms as diverse as yeast, worm, fly and fish, but it also reveals the potential of this short-lived fish as an animal model for pharmacological research. Moreover, being related to stickleback (Gasterosteus aculeatus) the "pufferfishes" Takifugu and Tetraodon, and even more closely related to medaka (Oryzias latipes), it can greatly beneficiate from the recent development of genomic resources for these fish models and in the future become a complete model system for the aging research community.
These fishes can become excellent models for aging studies. They can be employed to test the effects of experimental manipulation on aging at a pace comparable with that of Drosophila and to probe the effects of natural selection on the evolution of aging-related genes.

Answer: N. furzeri an interesting model system to investigate the effects of experimental manipulations on longevity and age-related pathologies.
N. furzeri could represent a model system for studying the genetic control of life-history traits in natural populations.
N. furzeri could be a very useful model for comparative genomics of aging.
It can be employed to test the effects of experimental manipulation on aging and apharmacological research.
Exact answer: aging research
Question: The CXCR2 receptor is targeted in cancer. Name five antagonists.

Context:
CXCR2 small-molecule antagonist (SB225002)
G31P, an antagonist against CXC chemokine receptors 1 and 2, inhibits growth of human prostate cancer cells in nude mice.
The CXCR2 antagonist, SCH-527123, shows antitumor activity
retreatment with the CXCR2 antagonist AZ10397767
The aim of this study was to investigate whether the CXCR2 antagonist, SCH-527123, inhibits colorectal cancer proliferation and if it can sensitize colorectal cancer cells to oxaliplatin both in vitro and in vivo.
we report that targeting CXCR2 and CXCR1 activity using orally active small molecule antagonist (SCH-527123, SCH-479833) inhibits human colon cancer liver metastasis mediated by decreased neovascularization and enhanced malignant cell apoptosis.
CXCR2-specific small molecule inhibitor (AZ10397767) to investigate the recruitment and function of human neutrophils in tumors

Answer: There are numerous CXCR2 receptor antagonists, such as SB225002, G31P, SCH-527123, AZ10397767, SCH-479833.
Exact answer: SB225002, G31P, SCH-527123, AZ10397767, SCH-479833
Question: Can the iPS cell technology be used in Fanconi anemia therapy?

Context:
We explain a protocol for the reproducible generation of genetically corrected iPSCs starting from the skin biopsies of Fanconi anemia patients using retroviral transduction with OCT4, SOX2 and KLF4
Before reprogramming, the fibroblasts and/or keratinocytes of the patients are genetically corrected with lentiviruses expressing FANCA.
Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells
Here we show that, on correction of the genetic defect, somatic cells from Fanconi anaemia patients can be reprogrammed to pluripotency to generate patient-specific iPS cells. These cell lines appear indistinguishable from human embryonic stem cells and iPS cells from healthy individuals
Most importantly, we show that corrected Fanconi-anaemia-specific iPS cells can give rise to haematopoietic progenitors of the myeloid and erythroid lineages that are phenotypically normal, that is, disease-free

Answer: iPS cell technology can be used for the generation of disease-corrected, patient-specific cells with potential value for cell therapy applications in Fanconi anemia.
Exact answer: yes
Question: What is TOPAZ1?

Context:
TOPAZ1, a germ cell specific factor, is essential for male meiotic progression
Topaz1 (Testis and Ovary-specific PAZ domain gene 1) is a germ cell specific gene highly conserved in vertebrates
Topaz1 is supposed to have a role during gametogenesis and may be involved in the piRNA pathway and contribute to silencing of transposable elements and maintenance of genome integrity
TOPAZ1, a novel germ cell-specific expressed gene conserved during evolution across vertebrates

Answer: TOPAZ1 is a novel germ cell-specific expressed gene conserved during evolution across vertebrates. Its PAZ-domain protein is abundantly expressed in the gonads during germ cell meiosis. The expression pattern of TOPAZ1, and its high degree of conservation, suggests that it may play an important role in germ cell development. Further characterization of TOPAZ1 may elucidate the mechanisms involved in gametogenesis, and particularly in the RNA silencing process in the germ line.
TOPAZ1 (Testis and Ovary-specific PAZ domain gene 1) is a germ cell specific factor that is essential for male meiotic progression. Topaz1 is supposed to have a role during gametogenesis and may be involved in the piRNA pathway and contribute to silencing of transposable elements and maintenance of genome integrity. It is highly conserved in vertebrates.